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From: Harry M. <man...@ho...> - 2001-01-29 20:02:18
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Greg, it's for the Sourceforge Web site to be the GeneX Face to the world, for release and dev work. "Greg D. Colello" wrote: > I must have missed something. I didn't understand what your email was about. -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: <ja...@op...> - 2001-01-29 20:00:47
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"Greg D. Colello" <gd...@nc...> writes: > It would be really cool if someone would take the responsibility > after each listserv thread or related threads, to summarize the I don't think anyone is going to volunteer for this, so unless it is *assigned* it won't get done. > It would even be cooler if instead each SUMMARY appeared in an FAQ > link, but it appears that SourceForge doesn't have an FAQ resource > for each project. This could be handled if we installed FAQ-o-Matic on the source forge site. Harry, would this be useful? jas. |
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From: <ja...@op...> - 2001-01-29 19:49:29
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Hey All, Here's a suggestion for keeping list quality high. That whenever we reply or forward to something, we edit the text of the message down to only what we need to quote. This may cost us an extra minute or two, but since there are ~10 or people subscribed to the list, it will save them quite a bit of time. > >From: Harry Mangalam <man...@ho...> > >X-Accept-Language: en > >MIME-Version: 1.0 > >To: genexdev at SF <gen...@li...> > >Content-Transfer-Encoding: 7bit > >Subject: [GeneX-dev] GeneX Sourceforge Web page template > >X-BeenThere: gen...@li... > >X-Mailman-Version: 2.0 > >List-Help: <mailto:gen...@li...?subject=help> > >List-Post: <mailto:gen...@li...> > >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, > <mailto:gen...@li...?subject=subscribe> > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> > >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, > <mailto:gen...@li...?subject=unsubscribe> > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> > >Date: Mon, 29 Jan 2001 09:24:50 -0800 We shouldn't need to quote anyone's headers, please. > >Cheers, > >Harry > > > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > > >_______________________________________________ > >Genex-dev mailing list > >Gen...@li... > >http://lists.sourceforge.net/lists/listinfo/genex-dev > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev please edit off other peoples signatures, as well as the auto-generated list signature. Thanks, jas. |
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From: Greg D. C. <gd...@nc...> - 2001-01-29 19:44:25
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To all: It would be really cool if someone would take the responsibility after each listserv thread or related threads, to summarize the results in an email whose subject starts with the key word SUMMARY: followed by the thread subject line. This occurred to me, because I looked at the SourceForge listserv for GeneX, and found the email list there somewhat bewildering. It would even be cooler if instead each SUMMARY appeared in an FAQ link, but it appears that SourceForge doesn't have an FAQ resource for each project. A summary item for each thread will probably cover our FAQ needs for now. Later we can turn the SUMMARY items into actual FAQ's. Greg |
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From: Todd P. <tf...@nc...> - 2001-01-29 19:41:51
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Will do tomorrow. ----- Original Message ----- From: "Harry Mangalam" <man...@ho...> To: <gen...@li...> Sent: Monday, January 29, 2001 10:38 AM Subject: Re: [GeneX-dev] Schema diagram? > But this one is slightly older than the current one (it still shows CSF, etc). > > Todd, if you can produce another ERWIN diagram, I'll put it out on the web and also try to create a 'dia' diagram of it or some other opensource UML editor so others can contrib to it > > "Greg D. Colello" wrote: > > > > Yes. See URL: > > > > http://www.ncgr.org/research/genex/schema.html > > > > Greg > > -- > Cheers, > Harry > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
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From: Greg D. C. <gd...@nc...> - 2001-01-29 19:30:30
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Harry: I must have missed something. I didn't understand what your email was about. Obviously you are building a front end web page, but for what? It seems like a useful organization of GeneX information, but it's hard to evaluate, when I don't know where it will appear. Greg >From: Harry Mangalam <man...@ho...> >X-Accept-Language: en >MIME-Version: 1.0 >To: genexdev at SF <gen...@li...> >Content-Transfer-Encoding: 7bit >Subject: [GeneX-dev] GeneX Sourceforge Web page template >X-BeenThere: gen...@li... >X-Mailman-Version: 2.0 >List-Help: <mailto:gen...@li...?subject=help> >List-Post: <mailto:gen...@li...> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=subscribe> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=unsubscribe> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> >Date: Mon, 29 Jan 2001 09:24:50 -0800 > >Please look at it and comment on the layout and especially what the nav bar should include. It will be turned into a shtml so the nav bar can be included everywhere and the color choices are >certainly up for discussion. As is the Header title graphics, but I do want it to be kept as simple as possible. > >Real content and live links are going in as soon as I send this and I think we can replace the currenplace holder by tonight or tomorrow. > >http://24.1.175.29/sf/index.hjm.html >-- >Cheers, >Harry > >Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > >_______________________________________________ >Genex-dev mailing list >Gen...@li... >http://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Harry M. <man...@ho...> - 2001-01-29 18:58:40
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"Jason E. Stewart" wrote: > > Hey Harry, > > Thanks for doing this. Comments: > * Canary yellow is a bit glaring (but you probably already know this) You think? But what about the Rcluster pages? :) yeah - I just stuck that in there for a target - I'll play around with some decent coloration. > * Where will the 'Home' URL point to? If not to NCGR, we should > include a toplevel link to GeneX@NCGR, which is maybe the 'Live > Demo' link? Look at it again. > * 'Get the Software', should probably contain *our* software, and we > should have another 'PreRequisite Software' section for R, xgobi, > etc Good Point - I'll divvy it between our SW and required software. > * 'Contacts', we should keep the genex-dev@ncgr private and only > publicize the genex-dev@sourceforge list. We also don't need to > publicize our individual emails. Anyone who wants them can get them > from the list archives our email us 'devel_name'@sourceforge. It > just invites more SPAM that I don't want. good point. Thanks. > Thanks, > jas. > > "Harry Mangalam" <man...@ho...> writes: > > > Please look at it and comment on the layout and especially what the nav bar should include. It will be turned into a shtml so the nav bar can be included everywhere and the color choices are > > certainly up for discussion. As is the Header title graphics, but I do want it to be kept as simple as possible. > > > > Real content and live links are going in as soon as I send this and I think we can replace the currenplace holder by tonight or tomorrow. > > > > http://24.1.175.29/sf/index.hjm.html > > -- > > Cheers, > > Harry > > > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > > > _______________________________________________ > > Genex-dev mailing list > > Gen...@li... > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: <ja...@op...> - 2001-01-29 18:04:29
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Hey Harry, Thanks for doing this. Comments: * Canary yellow is a bit glaring (but you probably already know this) * Where will the 'Home' URL point to? If not to NCGR, we should include a toplevel link to GeneX@NCGR, which is maybe the 'Live Demo' link? * 'Get the Software', should probably contain *our* software, and we should have another 'PreRequisite Software' section for R, xgobi, etc. * 'Contacts', we should keep the genex-dev@ncgr private and only publicize the genex-dev@sourceforge list. We also don't need to publicize our individual emails. Anyone who wants them can get them from the list archives our email us 'devel_name'@sourceforge. It just invites more SPAM that I don't want. Thanks, jas. "Harry Mangalam" <man...@ho...> writes: > Please look at it and comment on the layout and especially what the nav bar should include. It will be turned into a shtml so the nav bar can be included everywhere and the color choices are > certainly up for discussion. As is the Header title graphics, but I do want it to be kept as simple as possible. > > Real content and live links are going in as soon as I send this and I think we can replace the currenplace holder by tonight or tomorrow. > > http://24.1.175.29/sf/index.hjm.html > -- > Cheers, > Harry > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Harry M. <man...@ho...> - 2001-01-29 17:41:42
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But this one is slightly older than the current one (it still shows CSF, etc). Todd, if you can produce another ERWIN diagram, I'll put it out on the web and also try to create a 'dia' diagram of it or some other opensource UML editor so others can contrib to it "Greg D. Colello" wrote: > > Yes. See URL: > > http://www.ncgr.org/research/genex/schema.html > > Greg -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Harry M. <man...@ho...> - 2001-01-29 17:27:55
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Please look at it and comment on the layout and especially what the nav bar should include. It will be turned into a shtml so the nav bar can be included everywhere and the color choices are certainly up for discussion. As is the Header title graphics, but I do want it to be kept as simple as possible. Real content and live links are going in as soon as I send this and I think we can replace the currenplace holder by tonight or tomorrow. http://24.1.175.29/sf/index.hjm.html -- Cheers, Harry Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
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From: Todd P. <tf...@nc...> - 2001-01-29 17:15:19
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Another thing to add to the procedure: all CVS commits shall reference a =
Bugzilla item(s). The commit message should have a standard (agreed =
upon) form such as:=20
cvs commit -m "bug #1234: blah, blah" filename(s)
This allows for better change tracking.
Michael is right about this. The procedures are already there for this, =
we just haven't been sticking to them. Let me reiterate a couple of =
rules that we need to follow. =20
Nobody fixes anything that is not logged into bugzilla. That means that =
if you find a bug and fix it on your own, you log it into bugzilla =
yourself.
You fix bugs according to their bugzilla priority level. The priority =
levels are set after discussion with the group, so they should be =
followed. Basically they are our plan of attack, which we need to stick =
to.
Before you make any changes, check with the other developers and test =
your changes before commiting them to cvs.
I don't think we're too far off of this now, but we all need to be more =
cautious, and follow our procedures. We are now in a new phase for this =
project and these procedures are more important than ever now.
We will try to set priorities at our next meeting (tomorrow).
Lonny
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From: Greg D. C. <gd...@nc...> - 2001-01-29 16:38:51
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Yes. See URL: http://www.ncgr.org/research/genex/schema.html Greg >From: "Michael Pear" <mic...@ho...> >To: <gen...@li...> >MIME-Version: 1.0 >X-Priority: 3 >X-MSMail-Priority: Normal >X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 >Subject: [GeneX-dev] Schema diagram? >X-BeenThere: gen...@li... >X-Mailman-Version: 2.0 >List-Help: <mailto:gen...@li...?subject=help> >List-Post: <mailto:gen...@li...> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=subscribe> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=unsubscribe> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> >Date: Sat, 27 Jan 2001 14:48:54 -0800 > >Is there a current schema diagram available for the >GeneX DB? > >Regards, > >Michael Pear > |
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From: Todd P. <tf...@nc...> - 2001-01-28 22:22:59
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The schema is in dire need of sychronization with the actual Erwin = representation. The good thing is that there are nice reports produced = by Erwin which could probably be parsed and auto-compared to the actual = database tables. This task is my responsibility. Will figure out how to = work it in. Todd ----- Original Message -----=20 From: Michael Pear=20 To: gen...@li...=20 Sent: Saturday, January 27, 2001 3:48 PM Subject: [GeneX-dev] Schema diagram? Is there a current schema diagram available for the GeneX DB?=20 Regards, Michael Pear |
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From: <ja...@op...> - 2001-01-27 23:52:28
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"Michael Pear" <mic...@ho...> writes: > I'd like to offer some ideas based on my experience managing > software releases, albeit in a commercial environment, not open > source. The comments aren't meant to be directed at any of you > specifically...I've been very impressed with the responsiveness of > the team to issues I've encountered, and we could not be where we > are today at our site without your efforts! Thanks for you thoughts, Michael. I am grateful for the many aspects of your participation in this project, you have proved yourself to be an invaluable collaborator. Your experience in software development is far greater than mine, and so I read your words with great interest. I have been involved in the 'Free Software' Community (now the Open Source community) for almost 10 years, first as a user, then an addict, and finally a contributor and moderator. I'd like to add some of my own, limited, perspective to the discussion. <caveat> Before I start, however, I must add that this is 105% my own opinion, and has no reflection whatsoever on the goals/ideas/direction of NCGR. I am not one of the administrative leaders of the project, just a sometimes overzealous contributor. I joined shortly after NCGR, together with Harry began the project (almost two years ago). </caveat> Who is our intended audience? ============================= Ever since Harry and I put together the first grant for GeneX the idea was to run it as an OpenSource project. We were targeting labs who needed a resource like GeneX to solve their needs. These labs did not want to shell out $500+k for something like Resolver, they wanted to hire undergrad CS majors to slap together something for them in M$ Access. What was the scope of the project? ================================== We have intended this to be a *research* project, not a commercial software effort. The NSF grant clearly states that we will deliver a *prototype* system that enables researchers to store, analyze, and communicate their expression data. Given this perspective I can discuss your advice. > The fundamental precept of a release is that change is your > enemy. Now is not the time to catch up on those things that you > really wanted to get done for the release! First, in my mind there is a difference between a "Release" and "making code available". I believe that for our first public "release" we want to under-promise and over-deliver. We want to provide a basic system that gets people interested in the project, and most importantly a system that *works*. So your advice is particulary applicable to the development phase we are currently in. And ... Once we have our "Release", it is my intention to "make new code available" as often as possible. That is what anonymous CVS access is for. I work on a piece, and check that it works in my own micro-context, then I check it in to CVS. This access to daily updates radically changes the perspectives on bugs and releases. <aside> For example, using the debian package manager, I update my OS on a weekly basis, to grab any necessary packages that the maintainers have made available to fix certain performance or security issues, and since I run a PPC system, to grab new features. </aside> One of the pieces that will help this project succeed, is that I have spent a good amount of time designing and implementing pieces of this project so they can be upgraded independantly of one another. That is how I was able to fix many of your issues by making Bio-Genex-2.5.0 available. The problems were only in the Perl API code, so no need to cut a new "Release" of the entire Server. If the only way users could get updates was to re-run a complete Server install, we would die quickly. Because I plan to make new code available on a daily basis, I am completely unafraid of releasing code with bugs. I want to do what is reasonable to minimize the number and severity of the bugs, but this is *vastly* different than a commercial project that only releases new code twice a year. > I suggest a few things to consider: > > 1) Create a release checklist of bug fixes and any other changes you > decide must be in the release for the server + curation tool > together. Someone needs to act as the release manager, resisting > change and keeping the checklist..and you need to allow that > person to make a "no" decision regarding a proposed change! Greg, Lonny, and Todd have been doing this with curation tool for quite some time. They have also been using bugzilla quite effectively to keep track of bugs and fixes. I have been keeping very detailed ChangeLogs for all code modifications for the Server, but this is not good enough for a ReleaseNotes document, it is too low level. So I have just begun putting together the higher level notes as well. I haven't been using any bug-tracking for the Server code, and really need to begin. > 2) If you haven't already, create a CVS branch for the release and > only make changes in it according to the release. When the > release is done, then you can tag the branch as the release, and > merge in the development changes. Take your urges for more > dramatic change out in the development branch Currently, we have no stable branch only a development branch, this is a pain. This will be happily rectified as soon as we make the release, and the release becomes the official stable branch. > 3) Do regular "builds" of the system rather than patch. Changes have > a way of getting into test systems through patches that don't end > up in the source code tree! In the end, if you can't build it > from the CVS tree, then you can't reproduce the release. Good to re-hear this. Currently building the Server is run 100% from CVS: 1) make all code changes 2) 'cvs tag' with pre-release tag 3) 'cvs export' using release tag and run test build of Server 4) make any necessary code changes, check them into CVS 5) re-run 'cvs tag' with new tag 6) repeat 3-6 until it build cleanly 7) tar it up and ftp it to sourceforge Thanks again for your perspective, jas. |
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From: Michael P. <mic...@ho...> - 2001-01-27 22:46:15
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Is there a current schema diagram available for the GeneX DB?=20 Regards, Michael Pear |
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From: Todd P. <tf...@nc...> - 2001-01-27 18:01:58
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Excellent suggestions, Michael! We REALLY need a SQA person full-time to = support us on this. Peer reviews are another effective way to help = minimize the evils of SW change. I am an advocate of the SEI CMM = (sei.cmu.edu). ----- Original Message -----=20 From: Michael Pear=20 To: gen...@li...=20 Sent: Saturday, January 27, 2001 8:02 AM Subject: [GeneX-dev] Release management perspective... Hi GeneX Developers, I'd like to offer some ideas based on my experience managing software releases, albeit in a commercial environment, not open = source. The comments aren't meant to be directed at any of you specifically...I've = been very impressed with the responsiveness of the team to issues I've = encountered, and we could not be where we are today at our site without your efforts! The fundamental precept of a release is that change is your enemy. Now = is not the time to catch up on those things that you really wanted to get = done for the release! One analogy that I like is from "The Dyamics of = Software Development" by Jim McCarthy: "Shipping a product is like watching a large-sized serving of = quivering Jell-O. Gradually, the Jell-O slows its vibrations. But then = you fix a bunch of bugs, and it starts quivering frenetically again. = Then slowly, ever so slowly, the quivering subsides. You wait, focused = and primed, for the instant the Jell-O stops shaking. Then....you ship = it!" (I highly recommend this book as a whole, even if you suffer an = adverse physical reaction if you see "Microsoft Press" on the cover of a = book:-) The second precept is that you must make changes to get the release = out. But these must be made only with the application of judgment that = the change is aabsolutely necessary to make. I usually apply three = questions: 1) What is the impact of the bug or issue? 2) What is the effort involved? 3) What is the risk to the release of introducing the change? For example, often times we automatically fix a crash, even though it only affects 1% of users in .5% of situations and requires a = significant change in a central piece of code that affects 100's of code = paths, but ignore a nuisance bug that 100% of users experience, vitally = affects their perception of your software, and only requires one line of = code in a non-central location. Exaggerated, I'm sure, but you get the = point. I suggest a few things to consider: 1) Create a release checklist of bug fixes and any other changes you = decide must be in the release for the server + curation tool together. = Someone needs to act as the release manager, resisting change and = keeping the checklist..and you need to allow that person to make a "no" = decision regarding a proposed change! 2) If you haven't already, create a CVS branch for the release and = only make changes in it according to the release. When the release is done, then you can tag the branch as the release, and merge in the = development changes. Take your urges for more dramatic change out in the = development branch 3) Do regular "builds" of the system rather than patch. Changes have a = way of getting into test systems through patches that don't end up in = the source code tree! In the end, if you can't build it from the CVS tree, then you can't = reproduce the release. Releases have a way of dragging on...I know from personal experience. = Hope some of these tips help. Regards, Michael Pear |
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From: Michael P. <mic...@ho...> - 2001-01-27 15:00:03
|
Hi GeneX Developers, I'd like to offer some ideas based on my experience managing software releases, albeit in a commercial environment, not open source. = The comments aren't meant to be directed at any of you specifically...I've = been very impressed with the responsiveness of the team to issues I've = encountered, and we could not be where we are today at our site without your efforts! The fundamental precept of a release is that change is your enemy. Now = is not the time to catch up on those things that you really wanted to get done for the release! One analogy that I like is from "The Dyamics of = Software Development" by Jim McCarthy: "Shipping a product is like watching a large-sized serving of quivering = Jell-O. Gradually, the Jell-O slows its vibrations. But then you fix a = bunch of bugs, and it starts quivering frenetically again. Then slowly, = ever so slowly, the quivering subsides. You wait, focused and primed, = for the instant the Jell-O stops shaking. Then....you ship it!" (I highly recommend this book as a whole, even if you suffer an adverse = physical reaction if you see "Microsoft Press" on the cover of a book:-) The second precept is that you must make changes to get the release out. = But these must be made only with the application of judgment that the = change is aabsolutely necessary to make. I usually apply three = questions: 1) What is the impact of the bug or issue? 2) What is the effort involved? 3) What is the risk to the release of introducing the change? For example, often times we automatically fix a crash, even though it only affects 1% of users in .5% of situations and requires a significant = change in a central piece of code that affects 100's of code paths, but = ignore a nuisance bug that 100% of users experience, vitally affects = their perception of your software, and only requires one line of code in = a non-central location. Exaggerated, I'm sure, but you get the point. I suggest a few things to consider: 1) Create a release checklist of bug fixes and any other changes you = decide must be in the release for the server + curation tool together. = Someone needs to act as the release manager, resisting change and = keeping the checklist..and you need to allow that person to make a "no" = decision regarding a proposed change! 2) If you haven't already, create a CVS branch for the release and only make changes in it according to the release. When the release is done, then you can tag the branch as the release, and merge in the development = changes. Take your urges for more dramatic change out in the development = branch 3) Do regular "builds" of the system rather than patch. Changes have a = way of getting into test systems through patches that don't end up in = the source code tree! In the end, if you can't build it from the CVS tree, then you can't = reproduce the release. Releases have a way of dragging on...I know from personal experience. = Hope some of these tips help. Regards, Michael Pear |
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From: Harry M. <man...@ho...> - 2001-01-27 06:29:40
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Hi Michael,
OK - I've found it, altho it's a bit bizarre...
The CyberT C&E program tests for a param called TOOLOW and if not set, it is effectively endef or zero in a numeric comparison. Therefore anthing less than 0 (when it's not set) gets set to zero.
In the DB file data transfer, for some reason, TOOLOW never tests as 0 - it's undef but not zero (Jason can probably explain this).
I've patched CyberT to behave the way it should if the TOOLOW is supposed to be undef, but it's deeper than this.
The upshot is that in the file upload, the R lib never sees the negative numbers - they're always caught and converted to 0. In the DB pass-thru, the negative get passed to R where it chokes, so the
R lib has to be patched to fix this.
You get the weird bug of the day badge for this one.
The Paired CyberT won't be afected as it gets passed ratios, which will NOT be negative (unless you force them to be by insisting that they be formed by using these straight raw numbers...?)
So on to the author...
Tony, running the attached data set thru CYberT C+E, we get the following error for the reasons stated above. the reason for including negative numbers is that sometimes people want to include even
obviously bad data if it more accurately reflects the numbers coming off the scanner for their own reasons. So doitall() has to support this and it's choking here:
> library(hdarray,lib.loc='/var/genex/local/lib/R/library')
> ss <- read.table("/var/genex/tmp/genex/hda1874980579171/data",sep="\t")
> doitall(ss, 2, 4, 5, 7, 7, 0.25, 2)
Error in cov(x, y, use = use) : missing observations in cov/cor
there's no cov() in doitall, but there are lots of var() calls which I think share the same error message. I'll debug if you can't but you can do this 20x faster than I.
Can you give it a try?
HJM
Michael Pear wrote:
>
> Hi Harry,
>
> Things work for the Hatfield data set, but not for
> the one I submitted (ShearStress). I don't think the library location was
> an issue, there must be something where the library stuff is
> set during install. I can see a different error if I mess up the path info..
>
> Any problem with our data being "integer" data?
> I'm getting the error
>
> Error in cov(x, y, use = use) : missing observations in cov/cor
> In addition: There were 50 or more warnings (use warnings() to see the first 50)
> Execution halted
>
> Retrieves the columns of data with no problem. Any idea of what to look for in the data that would
> be considered "missing" observations? What if
> there are 0 observations for the control or experiment group because
> of negative/0 values for all the replicates?
>
> Let me know what I can test. Is there a debug flag I can turn on in
> R to trace the execution?
>
> Regards,
>
> Michael Pear
>
> ----- Original Message -----
> From: "Harry Mangalam" <man...@ho...>
> To: "Michael Pear" <mic...@ho...>
> Sent: Friday, January 26, 2001 6:40 PM
> Subject: Re: Data with negative numbers...
>
> > Hi Michael,
> >
> > I *WAS* joking about the insane locations..:) - and yup - we haven;t seen those odd locations so
> while the R libs were picked up in my install, I'm assuming that they were picked up from
> alternative
> > 'std' locations (altho I tried to wipe them out to see if it still worked and it still did...).
> >
> > Oh well, did the below fix work?
> >
> > hjm
> >
> >
> > Michael Pear wrote:
> > >
> > > Hi Harry,
> > > I found an rpm for R v 1.2 and downloaded that from the site
> > > in the INSTALL notes. Didn't do anything special other than that.
> > >
> > > The hdarray pieces were installed through the install-all.pl script.
> > > I didn't do anything outside of that script. Perhaps because I selected
> > > the "unusual" route of installiing under one root diretcory, you've not
> > > seen this before out of the install-all.pl script.
> > >
> > > M. Pear
> > >
> > > ----- Original Message -----
> > > From: "Harry Mangalam" <man...@ho...>
> > > To: "Michael Pear" <mic...@ho...>; "genexdev at SF" <gen...@li...>
> > > Sent: Friday, January 26, 2001 6:21 PM
> > > Subject: Re: Data with negative numbers...
> > >
> > > > Hi Michael,
> > > >
> > > > I thnk the reason is even simpler thatn this. Your installation of R doesn;t know where to
> find
> > > the proper libraries. R by default looks for them in /usr/local/lib/R..
> > > > but you installed it so that your R libs are in:
> > > > /var/genex1.0/local/lib/R/library/hdarray/R/hdarray
> > > >
> > > > The answer is to tell R how to find it which is done via the lib.loc arg to the library call.
> I
> > > never saw this before as my libs are stored in non-insane / system places, so I've just added
> that
> > > bit
> > > > and checked it in to CVS.
> > > >
> > > > if you want to change it in place, the mods are (for your install):
> > > >
> > > > in /your/cgi-bin/genex/cybert/
> > > >
> > > > CyberTDB-6.2.C+E.pl:352:
> > > > print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n";
> > > >
> > > > CyberTDB-6.2.paired.pl:407:
> > > > print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n";
> > > >
> > > > the way to debug this is to look in the hda.. dir created in your genex temporary dir this
> file
> > > typically contains a bunch of stuff
> > > >
> > > > -rw-r--r-- 1 apache apache 489 Jan 26 19:36 Rcommandfile
> > > > -rw-r--r-- 1 apache apache 162 Jan 26 19:36 Rerror
> > > > -rw-r--r-- 1 apache apache 37825 Jan 26 19:36 data
> > > > -rw-r--r-- 1 apache apache 174 Jan 26 19:36 xginput
> > > >
> > > > The Rcommandfile is the file containing the R commands that R tried to run. you can start R
> and
> > > run them one by one, just pasting them into the R shell. That's how I found that it couldn;t
> find
> > > your
> > > > hdarray lib (rather than the ubiquitous munge4R permission drecko.) The Rerror file contains
> the
> > > R errors, also useful sometimes when things appear to run but don;t get finished.
> > > >
> > > > the data file is... the data that R has to chew on . If it's 0 length or munged, we have a
> > > possible DB comms problem.
> > > >
> > > > xginput the input for xgobi and is a funny file that is created in 2 parts, the 1st is the
> header
> > > and is about 150 bytes, depending on the # of headers that are being written. Then the bulk of
> the
> > > > data is written by the munge4R.pl file which slices/dices/sorts/scrunches the data from the DB
> > > around until it's extruded in a form that xgobi can digest. The fact that it's short implies
> that
> > > the
> > > > data didn;t get writ.
> > > >
> > > > A complete family of files in the hda... dir would look like:
> > > >
> > > > -rw-r--r-- 1 nobody nobody 275934 Jan 26 18:01 ALLGENES
> > > > -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 CyberT.ps
> > > > -rw-r--r-- 1 nobody nobody 497 Jan 26 18:01 Rcommandfile
> > > > -rw-r--r-- 1 nobody nobody 301 Jan 26 18:01 Rerror
> > > > -rw-r--r-- 1 nobody nobody 275778 Jan 26 18:01 allgene.txt
> > > > -rw-r--r-- 1 nobody nobody 34423 Jan 26 18:01 data
> > > > -rw-r--r-- 1 nobody nobody 38187 Jan 26 18:01 temp
> > > > -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 temp.ps
> > > > -rw-r--r-- 1 nobody nobody 44045 Jan 26 18:01 xginput
> > > > -rw-r--r-- 1 nobody nobody 19417 Jan 26 18:01 xgobi-980560894.tar.gz
> > > >
> > > > These are mostly self-explanatory. Lemme know if you need more.
> > > >
> > > > Michael Pear wrote:
> > > > >
> > > > > Permissions were ok on merge4R.pl...mergem wasn't
> > > > > execute so I changed that.
> > > > >
> > > > > Logins were lost with our reinstall. It is probably best for
> > > > > you to work through me on this right now...and helps me
> > > > > become more aware of things. If it gets too tedious we'll
> > > > > get you a login.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Michael Pear
> > > > >
> > > > > ----- Original Message -----
> > > > > From: "Harry Mangalam" <man...@ho...>
> > > > > To: "Michael Pear" <mic...@ho...>
> > > > > Sent: Friday, January 26, 2001 4:44 PM
> > > > > Subject: Re: Data with negative numbers...
> > > > >
> > > > > > Hi Associate GeneX God,
> > > > > >
> > > > > > The problem looks to be in the transition from the DB retirieval to the anaytical tool and
> I
> > > bet
> > > > > it's the permissions on munge4R.pl I just tracked that bugger down on some other machines -
> > > check
> > > > > it -
> > > > > > it needs to be rx-all. It's fixed in the latest CVS, but you can just touch it gently and
> fix
> > > it
> > > > > in place.
> > > > > >
> > > > > > You (properly) locked down your machien - the old login you gave me doesn;t work anymmore,
> so
> > > I
> > > > > couldn;t log in ans see if this was the case or not. If you want me to be able to do that,
> call
> > > me
> > > > > with
> > > > > > a login and password. based on your past experience, please don't send it to me by email.
> > > > > >
> > > > > > Phones are still better for some things...
> > > > > >
> > > > > > hjm
> > > > > >
> > > > > >
> > > > > > > Michael Pear wrote:
> > > > > > >
> > > > > > > Hi Harry,
> > > > > > >
> > > > > > > I've got some local data loaded. It is priimary raw data with 3 replicates
> > > > > > > at 4 data points. When I run CyberT I get no results, possibly because of
> > > > > > > the negative numbers.
> > > > > > >
> > > > > > > I get the following message:
> > > > > > >
> > > > > > > Error in cov(x, y, use = use) : missing observations in cov/cor
> > > > > > > In addition: There were 50 or more warnings (use warnings() to see the first 50)
> > > > > > > Execution halted
> > > > > > >
> > > > > > > Is my interpretation correct? I imagine a good thing to consider is handling
> > > > > > > "off" data like this. Clearly, needs a more sophisticated background correction.
> > > > > > > Would some sort of filter be appropriate in the analysis to process those
> > > > > > > things that can be processed? How are zero values handled?
> > > > > >
> > > > > > Re: the analyses, yes, I'm going to have to come up with some better data filtering soon
> to
> > > handle
> > > > > this - in fact that was what my REAL job is supposed to be, not a SW developer (can you
> > > tell?!??).
> > > > > > What I'll be doing soon hopefully is changing the interface so that it a) gives you an
> > > indication
> > > > > of what kind of data it is and what parameters it will need to allow normalization and then
> b)
> > > allow
> > > > > > the user to apply this to the arrays under consideration.
> > > > > >
> > > > > > > Also, is my interpretation correct that I will end up with ratios (log?) of the
> > > > > > > experimental to control? I'll poke through the doc, but I'm a bit sketchy
> > > > > > > at this point on how the ratios are figured.
> > > > > >
> > > > > > Yes, you'll end up with ratios (called fold I believe) in the output.
> > > > > >
> > > > > > > I've been wondering about the background issue. It seems to me that if
> > > > > > > some gene's signal is within background, then you are basically saying
> > > > > > > that there is no detectable signal. Perhaps a stringent test of a gene
> > > > > > > being expressed relative to this is to pick a background threshold and
> > > > > > > set the gene with no signal to this threshold in evaluating the ratios.
> > > > > > > Thoughts?
> > > > > >
> > > > > > That's not bad in the absence of other data. This is the aching question - how do you
> > > calculate a
> > > > > ratio in the absence of a numerator (or worse, denominator). It may be that the better way
> of
> > > > > > representing this is the case of missing values is to just give an indicator of MAX or MIN
> or
> > > the
> > > > > absolute value of the detectable value. It's also possible to use the rank of the gene's
> > > expression
> > > > > > where it is detectable to give it a weighting.
> > > > > >
> >
> > --
> > Cheers,
> > Harry
> >
> > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
--
Cheers,
Harry
Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...
|
|
From: Michael P. <mic...@ho...> - 2001-01-27 04:23:48
|
We ran into this error when processing the control-bundle.xar. If it wasn't in the control-bundle-downloaded directory, it wasn't expanded and this error was the result of no xml file to parse. Not exactly the right message for the situation.. M. Pear ----- Original Message ----- From: "Greg D. Colello" <gd...@nc...> To: <gen...@li...> Sent: Friday, January 26, 2001 5:05 PM Subject: Re: [GeneX-dev] Re: DTD versions > Jason: > > I just tested this. No more version complaints, but now I get a different XML > SAX parser error: > > "The markup in the document preceding the root element must be well-formed." > > Now that's clear. > > Greg > > >Delivered-To: fix...@li...@fixme > >To: gen...@li... > >Cc: "Todd Peterson" <tf...@nc...> > >Subject: Re: [GeneX-dev] Re: DTD versions > >Mime-Version: 1.0 (generated by tm-edit 1.5) > >From: ja...@op... (Jason E. Stewart) > >X-BeenThere: gen...@li... > >X-Mailman-Version: 2.0 > >List-Help: <mailto:gen...@li...?subject=help> > >List-Post: <mailto:gen...@li...> > >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, > <mailto:gen...@li...?subject=subscribe> > >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> > >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, > <mailto:gen...@li...?subject=unsubscribe> > >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> > >Date: 26 Jan 2001 16:05:08 -0700 > > > >"Jason E. Stewart" <ja...@op...> writes: > > > >> Hey Todd, > >> > >> Short term to ensure things are working on genex.ncgr.org ASAP: > >> * I will modify the version strings on the DTD's in the installation so > >> they appear to be the version you're expecting > > > >This is fixed. Someone please try the curation tool and let me know if > >there's any problems. I'm sorry that I didn't realize sooner this was > >broken, too much email on a day that I was already frantically busy... > > > >jas. > > > > > >_______________________________________________ > >Genex-dev mailing list > >Gen...@li... > >http://lists.sourceforge.net/lists/listinfo/genex-dev > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev |
|
From: Michael P. <mic...@ho...> - 2001-01-27 04:01:06
|
Hi Harry, Things work for the Hatfield data set, but not for the one I submitted (ShearStress). I don't think the library location was an issue, there must be something where the library stuff is set during install. I can see a different error if I mess up the path info.. Any problem with our data being "integer" data? I'm getting the error Error in cov(x, y, use = use) : missing observations in cov/cor In addition: There were 50 or more warnings (use warnings() to see the first 50) Execution halted Retrieves the columns of data with no problem. Any idea of what to look for in the data that would be considered "missing" observations? What if there are 0 observations for the control or experiment group because of negative/0 values for all the replicates? Let me know what I can test. Is there a debug flag I can turn on in R to trace the execution? Regards, Michael Pear ----- Original Message ----- From: "Harry Mangalam" <man...@ho...> To: "Michael Pear" <mic...@ho...> Sent: Friday, January 26, 2001 6:40 PM Subject: Re: Data with negative numbers... > Hi Michael, > > I *WAS* joking about the insane locations..:) - and yup - we haven;t seen those odd locations so while the R libs were picked up in my install, I'm assuming that they were picked up from alternative > 'std' locations (altho I tried to wipe them out to see if it still worked and it still did...). > > Oh well, did the below fix work? > > hjm > > > Michael Pear wrote: > > > > Hi Harry, > > I found an rpm for R v 1.2 and downloaded that from the site > > in the INSTALL notes. Didn't do anything special other than that. > > > > The hdarray pieces were installed through the install-all.pl script. > > I didn't do anything outside of that script. Perhaps because I selected > > the "unusual" route of installiing under one root diretcory, you've not > > seen this before out of the install-all.pl script. > > > > M. Pear > > > > ----- Original Message ----- > > From: "Harry Mangalam" <man...@ho...> > > To: "Michael Pear" <mic...@ho...>; "genexdev at SF" <gen...@li...> > > Sent: Friday, January 26, 2001 6:21 PM > > Subject: Re: Data with negative numbers... > > > > > Hi Michael, > > > > > > I thnk the reason is even simpler thatn this. Your installation of R doesn;t know where to find > > the proper libraries. R by default looks for them in /usr/local/lib/R.. > > > but you installed it so that your R libs are in: > > > /var/genex1.0/local/lib/R/library/hdarray/R/hdarray > > > > > > The answer is to tell R how to find it which is done via the lib.loc arg to the library call. I > > never saw this before as my libs are stored in non-insane / system places, so I've just added that > > bit > > > and checked it in to CVS. > > > > > > if you want to change it in place, the mods are (for your install): > > > > > > in /your/cgi-bin/genex/cybert/ > > > > > > CyberTDB-6.2.C+E.pl:352: > > > print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n"; > > > > > > CyberTDB-6.2.paired.pl:407: > > > print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n"; > > > > > > the way to debug this is to look in the hda.. dir created in your genex temporary dir this file > > typically contains a bunch of stuff > > > > > > -rw-r--r-- 1 apache apache 489 Jan 26 19:36 Rcommandfile > > > -rw-r--r-- 1 apache apache 162 Jan 26 19:36 Rerror > > > -rw-r--r-- 1 apache apache 37825 Jan 26 19:36 data > > > -rw-r--r-- 1 apache apache 174 Jan 26 19:36 xginput > > > > > > The Rcommandfile is the file containing the R commands that R tried to run. you can start R and > > run them one by one, just pasting them into the R shell. That's how I found that it couldn;t find > > your > > > hdarray lib (rather than the ubiquitous munge4R permission drecko.) The Rerror file contains the > > R errors, also useful sometimes when things appear to run but don;t get finished. > > > > > > the data file is... the data that R has to chew on . If it's 0 length or munged, we have a > > possible DB comms problem. > > > > > > xginput the input for xgobi and is a funny file that is created in 2 parts, the 1st is the header > > and is about 150 bytes, depending on the # of headers that are being written. Then the bulk of the > > > data is written by the munge4R.pl file which slices/dices/sorts/scrunches the data from the DB > > around until it's extruded in a form that xgobi can digest. The fact that it's short implies that > > the > > > data didn;t get writ. > > > > > > A complete family of files in the hda... dir would look like: > > > > > > -rw-r--r-- 1 nobody nobody 275934 Jan 26 18:01 ALLGENES > > > -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 CyberT.ps > > > -rw-r--r-- 1 nobody nobody 497 Jan 26 18:01 Rcommandfile > > > -rw-r--r-- 1 nobody nobody 301 Jan 26 18:01 Rerror > > > -rw-r--r-- 1 nobody nobody 275778 Jan 26 18:01 allgene.txt > > > -rw-r--r-- 1 nobody nobody 34423 Jan 26 18:01 data > > > -rw-r--r-- 1 nobody nobody 38187 Jan 26 18:01 temp > > > -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 temp.ps > > > -rw-r--r-- 1 nobody nobody 44045 Jan 26 18:01 xginput > > > -rw-r--r-- 1 nobody nobody 19417 Jan 26 18:01 xgobi-980560894.tar.gz > > > > > > These are mostly self-explanatory. Lemme know if you need more. > > > > > > Michael Pear wrote: > > > > > > > > Permissions were ok on merge4R.pl...mergem wasn't > > > > execute so I changed that. > > > > > > > > Logins were lost with our reinstall. It is probably best for > > > > you to work through me on this right now...and helps me > > > > become more aware of things. If it gets too tedious we'll > > > > get you a login. > > > > > > > > Regards, > > > > > > > > Michael Pear > > > > > > > > ----- Original Message ----- > > > > From: "Harry Mangalam" <man...@ho...> > > > > To: "Michael Pear" <mic...@ho...> > > > > Sent: Friday, January 26, 2001 4:44 PM > > > > Subject: Re: Data with negative numbers... > > > > > > > > > Hi Associate GeneX God, > > > > > > > > > > The problem looks to be in the transition from the DB retirieval to the anaytical tool and I > > bet > > > > it's the permissions on munge4R.pl I just tracked that bugger down on some other machines - > > check > > > > it - > > > > > it needs to be rx-all. It's fixed in the latest CVS, but you can just touch it gently and fix > > it > > > > in place. > > > > > > > > > > You (properly) locked down your machien - the old login you gave me doesn;t work anymmore, so > > I > > > > couldn;t log in ans see if this was the case or not. If you want me to be able to do that, call > > me > > > > with > > > > > a login and password. based on your past experience, please don't send it to me by email. > > > > > > > > > > Phones are still better for some things... > > > > > > > > > > hjm > > > > > > > > > > > > > > > > Michael Pear wrote: > > > > > > > > > > > > Hi Harry, > > > > > > > > > > > > I've got some local data loaded. It is priimary raw data with 3 replicates > > > > > > at 4 data points. When I run CyberT I get no results, possibly because of > > > > > > the negative numbers. > > > > > > > > > > > > I get the following message: > > > > > > > > > > > > Error in cov(x, y, use = use) : missing observations in cov/cor > > > > > > In addition: There were 50 or more warnings (use warnings() to see the first 50) > > > > > > Execution halted > > > > > > > > > > > > Is my interpretation correct? I imagine a good thing to consider is handling > > > > > > "off" data like this. Clearly, needs a more sophisticated background correction. > > > > > > Would some sort of filter be appropriate in the analysis to process those > > > > > > things that can be processed? How are zero values handled? > > > > > > > > > > Re: the analyses, yes, I'm going to have to come up with some better data filtering soon to > > handle > > > > this - in fact that was what my REAL job is supposed to be, not a SW developer (can you > > tell?!??). > > > > > What I'll be doing soon hopefully is changing the interface so that it a) gives you an > > indication > > > > of what kind of data it is and what parameters it will need to allow normalization and then b) > > allow > > > > > the user to apply this to the arrays under consideration. > > > > > > > > > > > Also, is my interpretation correct that I will end up with ratios (log?) of the > > > > > > experimental to control? I'll poke through the doc, but I'm a bit sketchy > > > > > > at this point on how the ratios are figured. > > > > > > > > > > Yes, you'll end up with ratios (called fold I believe) in the output. > > > > > > > > > > > I've been wondering about the background issue. It seems to me that if > > > > > > some gene's signal is within background, then you are basically saying > > > > > > that there is no detectable signal. Perhaps a stringent test of a gene > > > > > > being expressed relative to this is to pick a background threshold and > > > > > > set the gene with no signal to this threshold in evaluating the ratios. > > > > > > Thoughts? > > > > > > > > > > That's not bad in the absence of other data. This is the aching question - how do you > > calculate a > > > > ratio in the absence of a numerator (or worse, denominator). It may be that the better way of > > > > > representing this is the case of missing values is to just give an indicator of MAX or MIN or > > the > > > > absolute value of the detectable value. It's also possible to use the rank of the gene's > > expression > > > > > where it is detectable to give it a weighting. > > > > > > > -- > Cheers, > Harry > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... |
|
From: Harry M. <man...@ho...> - 2001-01-27 02:24:10
|
Hi Michael, I thnk the reason is even simpler thatn this. Your installation of R doesn;t know where to find the proper libraries. R by default looks for them in /usr/local/lib/R.. but you installed it so that your R libs are in: /var/genex1.0/local/lib/R/library/hdarray/R/hdarray The answer is to tell R how to find it which is done via the lib.loc arg to the library call. I never saw this before as my libs are stored in non-insane / system places, so I've just added that bit and checked it in to CVS. if you want to change it in place, the mods are (for your install): in /your/cgi-bin/genex/cybert/ CyberTDB-6.2.C+E.pl:352: print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n"; CyberTDB-6.2.paired.pl:407: print CMD "library(hdarray, lib.loc = '/var/genex1.0/local/lib/R/library')\n"; the way to debug this is to look in the hda.. dir created in your genex temporary dir this file typically contains a bunch of stuff -rw-r--r-- 1 apache apache 489 Jan 26 19:36 Rcommandfile -rw-r--r-- 1 apache apache 162 Jan 26 19:36 Rerror -rw-r--r-- 1 apache apache 37825 Jan 26 19:36 data -rw-r--r-- 1 apache apache 174 Jan 26 19:36 xginput The Rcommandfile is the file containing the R commands that R tried to run. you can start R and run them one by one, just pasting them into the R shell. That's how I found that it couldn;t find your hdarray lib (rather than the ubiquitous munge4R permission drecko.) The Rerror file contains the R errors, also useful sometimes when things appear to run but don;t get finished. the data file is... the data that R has to chew on . If it's 0 length or munged, we have a possible DB comms problem. xginput the input for xgobi and is a funny file that is created in 2 parts, the 1st is the header and is about 150 bytes, depending on the # of headers that are being written. Then the bulk of the data is written by the munge4R.pl file which slices/dices/sorts/scrunches the data from the DB around until it's extruded in a form that xgobi can digest. The fact that it's short implies that the data didn;t get writ. A complete family of files in the hda... dir would look like: -rw-r--r-- 1 nobody nobody 275934 Jan 26 18:01 ALLGENES -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 CyberT.ps -rw-r--r-- 1 nobody nobody 497 Jan 26 18:01 Rcommandfile -rw-r--r-- 1 nobody nobody 301 Jan 26 18:01 Rerror -rw-r--r-- 1 nobody nobody 275778 Jan 26 18:01 allgene.txt -rw-r--r-- 1 nobody nobody 34423 Jan 26 18:01 data -rw-r--r-- 1 nobody nobody 38187 Jan 26 18:01 temp -rw-r--r-- 1 nobody nobody 240552 Jan 26 18:01 temp.ps -rw-r--r-- 1 nobody nobody 44045 Jan 26 18:01 xginput -rw-r--r-- 1 nobody nobody 19417 Jan 26 18:01 xgobi-980560894.tar.gz These are mostly self-explanatory. Lemme know if you need more. Michael Pear wrote: > > Permissions were ok on merge4R.pl...mergem wasn't > execute so I changed that. > > Logins were lost with our reinstall. It is probably best for > you to work through me on this right now...and helps me > become more aware of things. If it gets too tedious we'll > get you a login. > > Regards, > > Michael Pear > > ----- Original Message ----- > From: "Harry Mangalam" <man...@ho...> > To: "Michael Pear" <mic...@ho...> > Sent: Friday, January 26, 2001 4:44 PM > Subject: Re: Data with negative numbers... > > > Hi Associate GeneX God, > > > > The problem looks to be in the transition from the DB retirieval to the anaytical tool and I bet > it's the permissions on munge4R.pl I just tracked that bugger down on some other machines - check > it - > > it needs to be rx-all. It's fixed in the latest CVS, but you can just touch it gently and fix it > in place. > > > > You (properly) locked down your machien - the old login you gave me doesn;t work anymmore, so I > couldn;t log in ans see if this was the case or not. If you want me to be able to do that, call me > with > > a login and password. based on your past experience, please don't send it to me by email. > > > > Phones are still better for some things... > > > > hjm > > > > > > > Michael Pear wrote: > > > > > > Hi Harry, > > > > > > I've got some local data loaded. It is priimary raw data with 3 replicates > > > at 4 data points. When I run CyberT I get no results, possibly because of > > > the negative numbers. > > > > > > I get the following message: > > > > > > Error in cov(x, y, use = use) : missing observations in cov/cor > > > In addition: There were 50 or more warnings (use warnings() to see the first 50) > > > Execution halted > > > > > > Is my interpretation correct? I imagine a good thing to consider is handling > > > "off" data like this. Clearly, needs a more sophisticated background correction. > > > Would some sort of filter be appropriate in the analysis to process those > > > things that can be processed? How are zero values handled? > > > > Re: the analyses, yes, I'm going to have to come up with some better data filtering soon to handle > this - in fact that was what my REAL job is supposed to be, not a SW developer (can you tell?!??). > > What I'll be doing soon hopefully is changing the interface so that it a) gives you an indication > of what kind of data it is and what parameters it will need to allow normalization and then b) allow > > the user to apply this to the arrays under consideration. > > > > > Also, is my interpretation correct that I will end up with ratios (log?) of the > > > experimental to control? I'll poke through the doc, but I'm a bit sketchy > > > at this point on how the ratios are figured. > > > > Yes, you'll end up with ratios (called fold I believe) in the output. > > > > > I've been wondering about the background issue. It seems to me that if > > > some gene's signal is within background, then you are basically saying > > > that there is no detectable signal. Perhaps a stringent test of a gene > > > being expressed relative to this is to pick a background threshold and > > > set the gene with no signal to this threshold in evaluating the ratios. > > > Thoughts? > > > > That's not bad in the absence of other data. This is the aching question - how do you calculate a > ratio in the absence of a numerator (or worse, denominator). It may be that the better way of > > representing this is the case of missing values is to just give an indicator of MAX or MIN or the > absolute value of the detectable value. It's also possible to use the rank of the gene's expression > > where it is detectable to give it a weighting. > > |
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From: Greg D. C. <gd...@nc...> - 2001-01-27 01:05:27
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Jason: I just tested this. No more version complaints, but now I get a different XML SAX parser error: "The markup in the document preceding the root element must be well-formed." Now that's clear. Greg >Delivered-To: fix...@li...@fixme >To: gen...@li... >Cc: "Todd Peterson" <tf...@nc...> >Subject: Re: [GeneX-dev] Re: DTD versions >Mime-Version: 1.0 (generated by tm-edit 1.5) >From: ja...@op... (Jason E. Stewart) >X-BeenThere: gen...@li... >X-Mailman-Version: 2.0 >List-Help: <mailto:gen...@li...?subject=help> >List-Post: <mailto:gen...@li...> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=subscribe> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=unsubscribe> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> >Date: 26 Jan 2001 16:05:08 -0700 > >"Jason E. Stewart" <ja...@op...> writes: > >> Hey Todd, >> >> Short term to ensure things are working on genex.ncgr.org ASAP: >> * I will modify the version strings on the DTD's in the installation so >> they appear to be the version you're expecting > >This is fixed. Someone please try the curation tool and let me know if >there's any problems. I'm sorry that I didn't realize sooner this was >broken, too much email on a day that I was already frantically busy... > >jas. > > >_______________________________________________ >Genex-dev mailing list >Gen...@li... >http://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Greg D. C. <gd...@nc...> - 2001-01-27 00:57:12
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Jason: You forgot to mention my solution of passing the Curation Tool version number, as a parameter to the CGI login panel program, to check version compatibility with current server code. Greg >Delivered-To: fix...@li...@fixme >To: "Todd Peterson" <tf...@nc...> >Cc: gen...@li... >Mime-Version: 1.0 (generated by tm-edit 1.5) >From: ja...@op... (Jason E. Stewart) >Subject: [GeneX-dev] Re: DTD versions >X-BeenThere: gen...@li... >X-Mailman-Version: 2.0 >List-Help: <mailto:gen...@li...?subject=help> >List-Post: <mailto:gen...@li...> >List-Subscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=subscribe> >List-Id: GeneX Developers' List <genex-dev.lists.sourceforge.net> >List-Unsubscribe: <http://lists.sourceforge.net/lists/listinfo/genex-dev>, <mailto:gen...@li...?subject=unsubscribe> >List-Archive: <http://lists.sourceforge.net/archives//genex-dev/> >Date: 26 Jan 2001 15:25:18 -0700 > >Hey Todd, > >Good question. The versions changed for two reasons (neither of which >are all that convincing): >* The DTD's were moved from my CVS tree on my local machine to a new > CVS repository (Harry's machine), in a 'CVS-friendly' way that > unfortunately reset all version numbers to 1.1 >* Many comments were modified in the files to change all uses of GEML > to be GeneXML > >Now as to how to fix this. Long term, here are my suggestions: >1) The version numbers are automatically assigned by CVS, and until we > get everything into it's permanent home on SourceForge, these may > change again, and as such, are not stable >2) The dates, while also assigned by CVS are more stable, as they will > at least be guaranteed to increase no matter what archive they are > in. >3) I would recommend that the CT uses an approach similar to that of > xml2db, which is to accept a list of values and not just a single > value. This means that you could simply add to the list when a > minor version change takes place (such as the comment changes > above). >4) I'm not sure whether it's possible for you to have these in some > external configuration file instead of in the java source. That way > you could modify the configuration file and not need to recompile > any .class files > >Short term to ensure things are working on genex.ncgr.org ASAP: >* I will modify the version strings on the DTD's in the installation so > they appear to be the version you're expecting > >jas. > >"Todd Peterson" <tf...@nc...> writes: > >> When did versions of DTDs change? Here is what CT is expecting (direct from >> GEMLConstants.java): >> >> public static final String EXPECTED_GEML_VERSION = "1.15"; >> public static final String EXPECTED_USF_VERSION = "1.7"; >> public static final String EXPECTED_CSF_VERSION = "1.4"; >> public static final String EXPECTED_AMS_VERSION = "1.7"; >> public static final String EXPECTED_ALS_VERSION = "1.5"; >> public static final String EXPECTED_GEML_DATE = "2000/10/31"; >> public static final String EXPECTED_USF_DATE = "2000/10/17"; >> public static final String EXPECTED_CSF_DATE = "2000/10/17"; >> public static final String EXPECTED_AMS_DATE = "2000/10/17"; >> public static final String EXPECTED_ALS_DATE = "2000/10/17"; >> >> here's what I get from downloaded control bundle: >> >> <GENEXML cvs_id="$Id: genexml.dtd,v 1.1 2001/01/03 17:38:09 jes Exp $" >> date="2001/01/03" version="1.1"> >> >> <USF cvs_id="$Id: usf.dtd,v 1.1 2001/01/03 17:38:09 jes Exp $" >> date="2001/01/03" >> version="1.1"> >> >> <CSF cvs_id="$Id: csf.dtd,v 1.1 2001/01/03 17:38:09 jes Exp $" >> date="2001/01/03" >> version="1.1"> >> >> <ALS cvs_id="$Id: als.dtd,v 1.1 2001/01/03 17:38:09 jes Exp $" >> date="2001/01/03" >> version="1.1"> >> >> Todd Peterson >> NCGR >> mailto:tf...@nc... >> (505) 995-4417 > >_______________________________________________ >Genex-dev mailing list >Gen...@li... >http://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: Jiaye Z. <ze...@in...> - 2001-01-27 00:33:34
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Oh, sorry. CVS on harwin (harry's little thingie). You should have access to it? Jiaye Quoting Michael Pear <mic...@ho...>: > Hi Jiaye, > > CVS where? I don't think I have access to this, do I? > > Regards, > > Michael Pear > > ----- Original Message ----- > From: "Jiaye Zhou" <ze...@in...> > To: <gen...@li...>; "Michael Pear" > <mic...@ho...> > Sent: Friday, January 26, 2001 12:03 PM > Subject: Re: [GeneX-dev] xml2db.pl errors... > > > > > > Michael, > > > > The fixed version is in CVS now. Thanks again for point this out. > > > > jiaye > > > > Quoting Michael Pear <mic...@ho...>: > > > > > On the key removal for putative_csf_fk and nonunique_flag, > > > I consider what I did as a temporary kludge. I hope there is > > > a better permanent solution....Jiaye knows better than I how > > > these keys are set, from XML, programmatically, etc. and what > > > needs to be done to avoid their original creation. > > > > > > Regards, > > > > _______________________________________________ > > Genex-dev mailing list > > Gen...@li... > > http://lists.sourceforge.net/lists/listinfo/genex-dev > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev > |
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From: <ja...@op...> - 2001-01-26 23:22:44
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"Todd Peterson" <tf...@nc...> writes: > > 2) The dates, while also assigned by CVS are more stable, as they will > > at least be guaranteed to increase no matter what archive they are > > in. > > unless the date/time is changed. True. Really the problem is with the shifting repo. I could have been more careful about how I moved the files over to preserve the versions, but I didn't. Once CVS is stable on sourceforge this should create any issues. > > 4) I'm not sure whether it's possible for you to have these in some > > external configuration file instead of in the java source. That way > > you could modify the configuration file and not need to recompile > > any .class files > > could be put in properties file. Makes it simpler to deal with, I think > > Short term to ensure things are working on genex.ncgr.org ASAP: > > * I will modify the version strings on the DTD's in the installation so > > they appear to be the version you're expecting > > or i could make the mismatch less strict than it is now by just writing a > message to the console window instead of throwing an exception and stopping. > That's what I will do for now since versions might be messed up for a while. > When we settle things down, versions will be checked again somehow (most > likely not the way they are now). Sounds like a plan. jas. |
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