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From: Josef J. <ju...@cs...> - 2005-11-22 22:07:12
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In looking over the several typical output files of GenePix,
I see that most of the important values of these files map
to fields of the RAD.GenePixElementResult view:
GenePix RAD table
X ?
Y ?
Dia. RAD.GenePixElementResult.SPOT_DIAMETER
F635 Median RAD.GenePixElementResult.FOREGROUND_MEDIAN
F635 Mean RAD.GenePixElementResult.FOREGROUND_MEAN
F635 SD RAD.GenePixElementResult.FOREGROUND_SD
B635 Median RAD.GenePixElementResult.BACKGROUND_MEDIAN
B635 Mean RAD.GenePixElementResult.BACKGROUND_MEAN
B635 SD RAD.GenePixElementResult.BACKGROUND_SD
% > B635+1SD RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_ONE_SD
% > B635+2SD RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_TWO_SDS
F635 % Sat. RAD.GenePixElementResult.PERCENT_FOREGROUND_SATURATED
... ...
F Pixels RAD.GenePixElementResult.NUM_FOREGROUND_PIXELS
B Pixels RAD.GenePixElementResult.NUM_BACKGROUND_PIXELS
Circularity RAD.GenePixElementResult.CIRCULARITY
however as far as I can tell, there is no place in the view to put
the values of the columns that are labeled "X" and "Y" from a GenePix
output file. GenePix describes these values as follows
X the X-coordinate in µm of the center of the feature-indicator associated with
the feature, where (0,0) is the top left of the image.
Y the Y-coordinate in µm of the center of the feature-indicator associated with
the feature, where (0,0) is the top left of the image.
This is important information that we do not want to toss away.
Is this an oversight, or have I missed something?
I hope columns for these two values can be added to this table/view.
We will have to go a head an this columns in our locally installed
version of RAD anyways, as we need this.
Thanks Josef
Josef Jurek
Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...
voice: (773) 834-3985
fax: (773) 702-6648
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From: Junmin L. <ju...@pc...> - 2005-11-22 20:19:04
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It is kind of strange that plugin tries to query out extDBRelId based on id_url and version number. Juan, the whole deal about this is to get "external_database_release_id" for "MGED ontology version 1.2.0", so you should have the followings in your SRes. sres.externaldatabase.name="MGED ontology", sres.externaldatabaserelease has FK to the above entry. sres.externaldatabaserelease.version="1.2.0" A quick way to solve this is to simply comment out the code to get $extDbRelId for MO in the plugin, hard-code it with your sres.externaldatabaserelease.external_database_release_id. Then run it. --junmin On Tue, 22 Nov 2005, Juan Carlos Perin wrote: > $extDbUri is hard coded in insertontologyentry.pm to: > > http://mged.sourceforge.net/ontologies/MGEDOntology.daml > > The query fails because its looking at id_url in > sres.externaldatabaserelease and trying to match the URL with this ID which > is set to a number not the hard-coded URL above. So loading > StudyOntologyEntrydum_1.0.0.tab fails. I don't know if this is my error. I > could either forcefully change the value of url_id to http://mged.etc... Or > change the hard coded value in the module to the associated number for the > external database release value. I don't see a way to specify this value > when inserting the external database values. > > Juan > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Juan C. P. <bi...@ge...> - 2005-11-22 19:26:28
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$extDbUri is hard coded in insertontologyentry.pm to: http://mged.sourceforge.net/ontologies/MGEDOntology.daml The query fails because its looking at id_url in sres.externaldatabaserelease and trying to match the URL with this ID which is set to a number not the hard-coded URL above. So loading StudyOntologyEntrydum_1.0.0.tab fails. I don't know if this is my error. I could either forcefully change the value of url_id to http://mged.etc... Or change the hard coded value in the module to the associated number for the external database release value. I don't see a way to specify this value when inserting the external database values. Juan |
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From: Junmin L. <ju...@pc...> - 2005-11-22 15:50:12
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Hi, Amruta, The error you got "Fatal error: Call to undefined function: ora_logon()", means you don't have ORA module installed when you compile the php. Our RAD-SA in cbil here is using ora module against Oracle 10g. We don't have any problem. So looks like Oracle 10g DOES support ORA module. If you still want to use OCI, you might try global replacement the ora functions with corresponding oci functions. If you want me to further look at this problem. Please send me the followings, that may help me quickly solve your problem: 1. configuration string when you compile the php 2. the exact error message you got in php log. Thanks, ---junmin > The problem is not with php compilation; all oci functions are working fine. > Oracle 10g does not support ora_ functions. Hence, to use the > StudyAnnotator, we'll need to migrate the existing code to OCI ie rewrite > the ora_ fuction calls with equivalent oci ones. If you have any simpler > solution for this problem, please let me know. > > If you have a copy of StudyAnnotator with OCI, it will prove helpful as a > starting point/guideline. > > If anyone has an OCI version of StudyAnnotator, we'll appreciate if you can > share the code. > > Thanks, > Amruta > > Quoting Junmin Liu <ju...@pc...>: > >> Hi, Amruta, >> Yes, the OCI is more modern oracle php lib. At one point I migrated the >> code to use OCI, but I had to revert them back due to some reasons I >> cann't >> remember for now. Sorry about that, it could be that I cann't find a way >> to "fetch clob datatype from Oracle using OCI fucntion". >> >> Anyway, could you please check your php config? What is the options you >> use to compile PHP? Do you have the following two options: >> >> --with-oracle=/path/to/oracle/home/dir >> --with-oci8=/path/to/oracle/home/dir >> >> >> ---junmin >> |
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From: Junmin L. <ju...@pc...> - 2005-11-21 18:08:05
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Hi, Juan, You didn't do anything wrong. > DBD::Oracle::st execute failed: ORA-12899: value too large for column > "SRES"."SEQUENCEONTOLOGY"."DEFINITION" (actual: 1228, maximum: 1000) (DBD > ERROR: error possibly near <*> indicator at char 328 in ' > > I got this error earlier and found that, in fact, the definition file did > have entries that were too large. Should I extend the size of the field? Or > use the lighter sofa.definitions file? Or am I doing something wrong? Depending on how big the definition, you can either expand the column size in your db and file a bug in GUS bug tracker on this, or you can use shorter version. --junmin |
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From: Juan C. P. <bi...@ge...> - 2005-11-21 16:12:54
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In step 6 of loading the bootstrap data for RAD I've manually downloaded the so.definition file from song.sourceforge. The CVS site is not working for me on any machine, when I try logging in, it asks for a password, I press return and it just hangs until it eventually times out and aborts the connection attempt. The so.definition file is version 1.42. When I attempt to load the data using GUS::Supported::Plugin::InsertSequenceOntology I get: DBD::Oracle::st execute failed: ORA-12899: value too large for column "SRES"."SEQUENCEONTOLOGY"."DEFINITION" (actual: 1228, maximum: 1000) (DBD ERROR: error possibly near <*> indicator at char 328 in ' I got this error earlier and found that, in fact, the definition file did have entries that were too large. Should I extend the size of the field? Or use the lighter sofa.definitions file? Or am I doing something wrong? Thanks! Juan |
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From: John E. B. <jbr...@pc...> - 2005-11-17 20:03:58
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Hi Juan - Yes, that plugin requires the perl module... XML::LibXML The argument 'inFile' is expecting the daml file to be parsed... From documentation... inFile A daml file of MGED Ontology Terms and Relationships John > I've run into another speedbump... > > I get an error running InsertOntologyTermsAndRelationships. For some reason > its having locating some XML libraries. I've installed everything required > by GUS's install documentation. I get: > > Can't locate XML/LibXML.pm in @INC etc... > > I've tried to figure out if its a minor problem I'm missing, but am still > lost. Strangely, when I add +create to register the plugin it seems to work > okay, and --help with +create in the statement returns the help properly, > while ga GUS::Supported::etc.. --help does not. > > Also, the help doesn't specify how to use the daml file with the plugin, is > it the same as the others with --inputFile? > > And just a very minor note: The documentation > (README_StudyOntologyEntryDump_1.0.0) has a typo. The plugin name needs a > capitalized A for the And to match the actual plugin name. > > Juan > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Juan C. P. <bi...@ge...> - 2005-11-17 19:27:52
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I've run into another speedbump... I get an error running InsertOntologyTermsAndRelationships. For some reason its having locating some XML libraries. I've installed everything required by GUS's install documentation. I get: Can't locate XML/LibXML.pm in @INC etc... I've tried to figure out if its a minor problem I'm missing, but am still lost. Strangely, when I add +create to register the plugin it seems to work okay, and --help with +create in the statement returns the help properly, while ga GUS::Supported::etc.. --help does not. Also, the help doesn't specify how to use the daml file with the plugin, is it the same as the others with --inputFile? And just a very minor note: The documentation (README_StudyOntologyEntryDump_1.0.0) has a typo. The plugin name needs a capitalized A for the And to match the actual plugin name. Juan |
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From: Elisabetta M. <man...@pc...> - 2005-11-15 20:30:31
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Hi Juan, sorry, I should have clarified this in the announcement. There are some plugins that have been updated or added to the list of plugins from the GUS 3.5 release. So you want to use the trunk of the GUS svn repository to this end. If you go to http://www.gusdb.org/download.php you'll see in the section "Source Repository" a command that will enable you to check out the trunk in way that will automatically set up your $GUS_HOME, $PROJECT_HOME, etc. For any plugin referred to by the RAD/RADSA documentation you'll want to get the code from this svn repository. Elisabetta --- On Tue, 15 Nov 2005, Juan Carlos Perin wrote: > Upon attempting to setup today's release, I'm having some trouble loading > the bootstrap ontologies. I'm following the instructions to load > ontolRelTypeTerms.txt using > > GUS::Supported::Plugin::InsertOntologyRelationshipType > > First thing I found was that this plugin is actually in GUS::Community for > me, I'm not sure if that changed recently. Then, when I do run it with > --help to see its usage, or with any flags, I get: > > Can't locate object method "new" via package > "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1. > > Am I missing something obvious? > > Juan > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Junmin L. <ju...@pc...> - 2005-11-15 20:28:26
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Hi, > Upon attempting to setup today's release, I'm having some trouble loading > the bootstrap ontologies. I'm following the instructions to load > ontolRelTypeTerms.txt using > > GUS::Supported::Plugin::InsertOntologyRelationshipType Yes, it should be "Supported". > First thing I found was that this plugin is actually in GUS::Community for > me, I'm not sure if that changed recently. Then, when I do run it with It was first in Community, then move to Supported, but the plugin developer probably forgot deleting the Community version. > > Can't locate object method "new" via package > "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1. If you see any this kind of error, normally it indicate the wrong package name defined in the plugin file. So you should run "GUS::Supported::Plugin::InsertOntologyRelationshipType". ---junmin |
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From: Juan C. P. <bi...@ge...> - 2005-11-15 20:19:53
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Upon attempting to setup today's release, I'm having some trouble loading the bootstrap ontologies. I'm following the instructions to load ontolRelTypeTerms.txt using GUS::Supported::Plugin::InsertOntologyRelationshipType First thing I found was that this plugin is actually in GUS::Community for me, I'm not sure if that changed recently. Then, when I do run it with --help to see its usage, or with any flags, I get: Can't locate object method "new" via package "GUS::Community::Plugin::InsertOntologyRelationshipType" at (eval 8) line 1. Am I missing something obvious? Juan |
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From: Elisabetta M. <man...@pc...> - 2005-11-15 17:01:34
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Apologies if you receive this message multiple times, it is sent to various mailing lists. This is to let you know that a release of the RAD Study-Annotator compatible with GUS 3.5 is now available at http://www.cbil.upenn.edu/downloads/RAD/ This is in the tarball named RADSA_2.0.0.tar.gz In this tarball you will find a README_2.0.0 file with detailed instructions on installation and pointers to further instructions and dump files to load bootstrap data. Elisabetta |
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From: Junmin L. <ju...@pc...> - 2005-11-15 16:25:16
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Hi,Juan Can you provide me the following information? 1. the web link to your RAD SA? 2. the log message from your php log file? 3. what exactly happend to your RAD SA, describing the steps and the problem you got., saying something like this: "after I fill in user name and password and then hit submit button in login form, nothing happen." --junmin On Tue, 15 Nov 2005, Juan Carlos Perin wrote: > Hello, > > I am currently working on making sure our PHP and Apache are configured > properly for RAD. I've installed PHP5 and Apache2 and with OCI8 support > etc.. I turned on registered_globals in PHP.ini for RAD to work without > errors or notices, but still get a 'notice' problem with the $loginError > variable in login.php. I get the same 'notice' when accessing the > user_registration.php page, which occurs for all the variables set in the > include.php file for the session. > > I think there may be something wrong in my php.ini file regarding sessions, > but am not sure what. Session files seem to be saving to /tmp just fine, > and permissions are ok. If this is a php setting then I'd like to fix it, > if its something I won't have to worry about with the upcoming RAD release, > then I'll just be patient. If you have any advice, I really appreciate it. > Thank you! > > Juan > BIC > Children's hospital of Philadelphia > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Juan C. P. <bi...@ge...> - 2005-11-15 16:05:20
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Hello, I am currently working on making sure our PHP and Apache are configured properly for RAD. I've installed PHP5 and Apache2 and with OCI8 support etc.. I turned on registered_globals in PHP.ini for RAD to work without errors or notices, but still get a 'notice' problem with the $loginError variable in login.php. I get the same 'notice' when accessing the user_registration.php page, which occurs for all the variables set in the include.php file for the session. I think there may be something wrong in my php.ini file regarding sessions, but am not sure what. Session files seem to be saving to /tmp just fine, and permissions are ok. If this is a php setting then I'd like to fix it, if its something I won't have to worry about with the upcoming RAD release, then I'll just be patient. If you have any advice, I really appreciate it. Thank you! Juan BIC Children's hospital of Philadelphia |
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From: Junmin L. <ju...@pc...> - 2005-11-10 16:33:48
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Hi, Amruta, Yes, the OCI is more modern oracle php lib. At one point I migrated the code to use OCI, but I had to revert them back due to some reasons I cann't remember for now. Sorry about that, it could be that I cann't find a way to "fetch clob datatype from Oracle using OCI fucntion". Anyway, could you please check your php config? What is the options you use to compile PHP? Do you have the following two options: --with-oracle=/path/to/oracle/home/dir --with-oci8=/path/to/oracle/home/dir ---junmin On Wed, 9 Nov 2005, Amruta Joshi wrote: > Hi, > > We have installed GUS & have some basic data in it. We are using Oracle 10g > (Release 10.1). > > I have compiled the Study-Annotator for entering study-related data. However, > all the ora_ calls in the php files (likeora_logon, ora_getColumn etc.) fail. > I keep getting the error: > Fatal error: Call to undefined function: ora_logon() > > The function ociLogon works just fine. It seems that Oracle 10g supports only > OCI calls and not ora_ functions, which means I may have to rewrite chunks of > code that use ora_ calls. > Is there a better alternative to this? > Is Study-Annotator also made available with the new OCI calls? > I'm using the Study-Annotator source code from > http://www.cbil.upenn.edu/downloads/RAD/ > > Please reply soon, we need to get this working asap. > > thanks, > Amruta > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Elisabetta M. <man...@pc...> - 2005-11-09 12:12:26
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Hi Amruta, the RAD study annotator (RADSA) tarballs currently available at the donwload site you indicated below are both for previous version of GUS (< 3.5). A tarball for a RADSA compatible with GUS 3.5 will be released probably next week or early the following week and I'll send an announcement as soon as that occurs. Regarding the specific error and Oracle, I had a look at the code for the function that is used to connect to the db in the upcoming release (which we have been testing and using here in the past month and which works for us). It appears that it still uss ora_logon (albeit I see a commented out OCILogon call). I'll let Junmin, here cc-ed comment on this. Elisabetta --- On Wed, 9 Nov 2005, Amruta Joshi wrote: > Hi, > > We have installed GUS & have some basic data in it. We are using Oracle 10g > (Release 10.1). > > I have compiled the Study-Annotator for entering study-related data. However, > all the ora_ calls in the php files (likeora_logon, ora_getColumn etc.) fail. > I keep getting the error: > Fatal error: Call to undefined function: ora_logon() > > The function ociLogon works just fine. It seems that Oracle 10g supports only > OCI calls and not ora_ functions, which means I may have to rewrite chunks of > code that use ora_ calls. > Is there a better alternative to this? > Is Study-Annotator also made available with the new OCI calls? > I'm using the Study-Annotator source code from > http://www.cbil.upenn.edu/downloads/RAD/ > > Please reply soon, we need to get this working asap. > > thanks, > Amruta > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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From: Amruta J. <am...@st...> - 2005-11-09 10:28:26
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Hi,
We have installed GUS & have some basic data in it. We are using Oracle =
10g=20
(Release 10.1).
I have compiled the Study-Annotator for entering study-related data.=20
However, all the ora_ calls in the php files (likeora_logon, =
ora_getColumn=20
etc.) fail. I keep getting the error:
Fatal error: Call to undefined function: ora_logon()
The function ociLogon works just fine. It seems that Oracle 10g supports =
only OCI calls and not ora_ functions, which means I may have to rewrite =
chunks of code that use ora_ calls.
Is there a better alternative to this?
Is Study-Annotator also made available with the new OCI calls?
I'm using the Study-Annotator source code from=20
http://www.cbil.upenn.edu/downloads/RAD/
Please reply soon, we need to get this working asap.
thanks,
Amruta
--
Amruta Joshi
Research Assistant,
Relman Lab, Stanford University.
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From: Elisabetta M. <man...@pc...> - 2005-11-03 21:48:26
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Juan, probably Mike or Junmin can best address the specific php issues you are having. An important note related to the RAD StudyAnnotator (RADSA) is that the tarballs available at the RAD download site for the RADSA refer to versions of GUS preceding 3.5, so not all forms will work with 3.5. We should be releasing a RADSA tarball compatible with GUS 3.5 within the next couple of weeks. I'll send out an announcement when we do. Elisabetta --- On Thu, 3 Nov 2005, Juan Carlos Perin wrote: > I've installed GUS with no problems on our Dell running Advance Server 3. > Gus was built on oracle 10g. We're running Apache2 and PHP 4.2.3 by Zend. > We initially got a warning about sessionside.bug_compat, which I turned off > in php.ini and it got rid of the message. When I try to go to the > user_registration.php I get a blank page. If I try php user_registration on > the command line I get the following: > > Content-type: text/html > X-Powered-By: PHP/4.3.2 > Set-Cookie: PHPSESSID=0f2bff448ed776fbb19ccbca905fd6e9; path=/ > Expires: Thu, 19 Nov 1981 08:52:00 GMT > Cache-Control: no-store, no-cache, must-revalidate, post-check=0, > pre-check=0 > Pragma: no-cache > > I'm not sure what to make of this. Everything I find points at a cookie > problem but I've cleared my cache and done all that I'm aware of to avoid > it. This is probably something simple, but I'm not seeing it. Any help is > greatly appreciated. > > Juan Perin > Children's Hospital of Philadelphia > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Juan C. P. <bi...@ge...> - 2005-11-03 20:14:28
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I've installed GUS with no problems on our Dell running Advance Server 3. Gus was built on oracle 10g. We're running Apache2 and PHP 4.2.3 by Zend. We initially got a warning about sessionside.bug_compat, which I turned off in php.ini and it got rid of the message. When I try to go to the user_registration.php I get a blank page. If I try php user_registration on the command line I get the following: Content-type: text/html X-Powered-By: PHP/4.3.2 Set-Cookie: PHPSESSID=0f2bff448ed776fbb19ccbca905fd6e9; path=/ Expires: Thu, 19 Nov 1981 08:52:00 GMT Cache-Control: no-store, no-cache, must-revalidate, post-check=0, pre-check=0 Pragma: no-cache I'm not sure what to make of this. Everything I find points at a cookie problem but I've cleared my cache and done all that I'm aware of to avoid it. This is probably something simple, but I'm not seeing it. Any help is greatly appreciated. Juan Perin Children's Hospital of Philadelphia |
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From: Elisabetta M. <man...@pc...> - 2005-10-03 01:47:16
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Hi Sucheta, here is the way it works: 1. Entries in ElementResultImp point to Quantifications (which in turn point to the image analysis protocols); Quantifications point to Acquisitions (which in turn point to scanning protocols); Acquisitions point to Assays (which in turn point to the Arrays and to hybridization protocols). 2. An Assay corresponds to a one or two channel hybridization, so it will involve the RNA samples (or more precisely the labeled extracts obtained from these samples) that are hybridized to it. 3. Information about samples is stored in the various Biomaterial tables which include the Treatment tables. One can store the whole process from the original BioSource (e.g. "mouse", "mouse liver", "cell culture dish") to derived BioSamples (e.g. aliquots, RNAs, intermediate treatments etc.) to derived (from the BioSamples) LabeledExtracts. Each such derivation corresponds to a treatment stored in the Treatment table. Treatment points to the *output* of the treatment. BioMaterialMeasurement points to Treatment and to the *input* of that Treatment). This is pretty much straight from the MAGE model. For concrete examples of these, you might look at the 3 Examples at https://www.cbil.upenn.edu/RAD/tutorial/ModuleIII.html. 4. Each Assay is linked to all BioMaterials (BioSources, BioSamples, LabeledExtracts) corresponding to it via the AssayBioMaterial table. There is also a redundant table (which can be useful to expedite queries) which links each Assay to the LabeledExtracts corresponding to it (i.e. the last step in the chain from BioSources to LabeledExtracts). Thus to go from ElementResultImp to Treatments attached to the assay at hand, one goes up to Assay through Quantifications->Acquisitions->Assay, then can get all BioMaterials relative to that Assay through AssayBioMaterial, then get the Treatments pointing to those BioMaterials. Hope this helps. Elisabetta --- On Sun, 2 Oct 2005, Sucheta Tripathy wrote: > Hello Group, > > Another question. Since we have a large number of experiments and as I > understand we describe the treatment to each biological material in > RAD::Treatment table(Hope that is the way). However, I don't know how can I > link the raw .cel data for each experiment, that goes to ElementResultImp to > the Treatment table. > > Many thanks > > Sucheta > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Sucheta T. <su...@vb...> - 2005-10-03 00:07:28
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Hello Group, Another question. Since we have a large number of experiments and as I understand we describe the treatment to each biological material in RAD::Treatment table(Hope that is the way). However, I don't know how can I link the raw .cel data for each experiment, that goes to ElementResultImp to the Treatment table. Many thanks Sucheta |
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From: Sucheta T. <su...@vb...> - 2005-10-02 17:22:03
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Hi Group, Where can I find the old GUS-RAD schema browser. Thanks a lot. Sucheta |
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From: Elisabetta M. <man...@pc...> - 2005-04-19 18:34:34
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Hi Sucheta, the tables named RAD3.Analysis*** can be used to store downstream analyses (and with GUS 3.5 they will also be used to store upstream, i.e. preprocessing analyses, eliminating the Process*** tables). The RAd3.LogicalGroup*** tables can be used to store the input to an analysis (e.g. a group of quantification_ids, etc), this is linked to the analysis itself via RAD3.AnalysisInput. The results are stored in appropriate views for RAD3.AnalysisResultImp. By downstream analyses here we mean analyses like differential_expression, clustering, etc. Currently we have implemented views of AnalysisResultImp aimed to store mostly various kinds of differential_expression analyses, e.g. RAD3.SAM, RAD3.ArrayStatTwoConditions (we also have another view: DataTransformationResult which is devoted to the upcoming storage of pre-processed data). But the Analysis tables are flexible enough to accomodate other kinds of analyses. In our instance so far we have not been storing clustering results, but with appropriate views of AnalysisResultImp this should be doable. Let me first give you an example of how the results of SAM (differential expression) are stored in RAD. Say that you applied SAM to find differentially expressed genes between two conditions: C1 and C2. Say you have 4 assay per conditions and for simplicity that these were AffyMetrixMAS5.0 results: INPUT: You have some flexibility here. One option is to create two logical groups, one representing the 4 quantification_ids for C1 (LogicalGroupLink will identify each member of this group) and one to represent those for C2. (An alternative is to just create one Logical group to represent the group of all 8 quantification_ids for these 8 Affy result sets and then to use LogicalGroupLink.order_num to distinguish C1 and C2.) RESULTS: You would then create entries in AnalysisInput to link all logical groups input into the analysis to the analysis_id for this SAM run. AnalysisParam and AnalysisQCParam can be used to store any analysis parameter (or qc param) setting. Finally in the RAD3.SAM view of AnalysisResultImp you would store the results as illustrated in http://www.gusdb.org/cgi-bin/schemaBrowser?db=CBILBLD&table=RAD3::SAM&path=RAD3::SAM This is to illustrate the flexibility of these tables. For clustering you could devise a similar flow, albeit the detail will have to be worked out. E.g. for k-means clustering: Logical group could be used to store all quantification_ids (or analysis_ids, if the input is processed data) input into the clustering. Then an appropriate view of AnalysisResultImp would use (table_id, row_id) to denote the spot on the array to which the result refers and it could have a field say cluster_number to indicate to which cluster that spot belongs. Or something in this spirit. For hierarchical clustering a slightly more complex view would have to be designed. Hope this helps. Elisabetta P.S. I'm not too clear on the second part of your question: we store normalized data (formerly in the Process*** tables and now in the Analysis tables). Typically for each assay you would have as many results as spots on the chip, so I'm not clear on the 1.3 million per chip. If a chip say has 20,000 spots and you are using the analysis tables (DataTransformationResult), for this chip you would have 20,000 entries in this view plus a few sparse entries to fill in LogicalGroup, AnalysisInput, etc. So far we have had no problems storing our normalized data (even we we used the Process*** tables), but I guess it all depends on how many studies you are storing in your instance of RAD. > > We are currently planning to conduct more than one statistical analysis to a > particular dataset. However, I could not find a place to store them. > Similarly, if we do multiple types of clustering where the data can be > stored. > > We have another concern also about the data size and the query performance. > Our per chip one normalization method adds 1.3 million records, so if we have > several methods, then we will end up having several gigs of record. > > Do you have any issues with this. > > Many thanks > > Sucheta |
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From: Sucheta T. <su...@vb...> - 2005-04-19 17:47:59
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Hi Elisabetta, How are you doing? We are currently planning to conduct more than one statistical analysis to a particular dataset. However, I could not find a place to store them. Similarly, if we do multiple types of clustering where the data can be stored. We have another concern also about the data size and the query performance. Our per chip one normalization method adds 1.3 million records, so if we have several methods, then we will end up having several gigs of record. Do you have any issues with this. Many thanks Sucheta |
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From: Elisabetta M. <man...@pc...> - 2004-12-23 17:02:59
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This is an update on my Dec 8 email attached below. We have completed this implementation at CBIL. Here are modifications to the points I had made on my previous email: Point 2. We ended up creating RAD3.AssayAnalysis (linking) table instead of RAD3.StudyAnalysis table. Point 3. We have created this view. Point 5. How to deal with the input LogicalGroup is fairly flexible and different instances of GUS might decide to have different policies. Here is a snapshot of a few initial policies we are using at CBIL to this end: * Input LogicalGroups for DataTransformationResult analyses will not be nested, i.e. no input will be a LogicalGroup consisting itself of LogicalGroups. * For processes which are simple normalizations of a given quantification (or of a pair of quantifications for 2-channel data), the input to the analysis will be just ONE LogicalGroup consisting of that quantification (resp. pair of quantifications). * If the processing is normalization of log ratios in each of TWO 2-channel assays, followed by dye-swap merging, the input will be TWO LogicalGroups, each consisting of 2 quantifications: one logical group for the two samples that represent the numerator in the resulting dye-swap combination and the other for those representing the two samples that represent the denominator. Note that in this scenario we won't be grouping together the 2 quantifications (Cy5 and Cy3) that belong to the same assay. * If the processing is normalization of log ratios in each of n 2-channel assays, the input will be n LogicalGroups, one for each pair of quantifications corresponding to the same assay. Point 6. The AnalysisResultLoader plugin has been modified to deal with the new tables/view created and committed to the GUS/RAD cvs at Sanger. Documentation is at http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-AnalysisResultLoader.html Wishing a nice holiday and a happy New Year to everyone, Elisabetta --- On Wed, 8 Dec 2004, Elisabetta Manduchi wrote: > > Here at CBIL we have decided to deprecate the usage of the tables > RAD3.Process*** and to utilize instead a new view of RAD3.AnalysisResultImp > to store the results of a series of DataTransformation protocols. The > Analysis tables were created subsequently to the Process tables and have a > more mature layout, which should facilitate queries. They were originally > created to store down-stream analysis results (e.g. for differential > expression or clustering) but they are also suitable for pre-processing > result storage. > The following describes what we are implementing: > > 1. We have created a RAD3.ProtocolStep table to identify protocols consisting > of an ordered series of (sub) protocols. Every protocol of the latter form is > linked through RAD3.ProtocolStep to its components. Its type will be > "transformation_protocol_series" (DataTransformationProtocolType). > > 2. We'll create a linking table RAD3.StudyAnalysis to facilitate queries. > > 3. We'll create a new view of RAD3.AnalysisResultImp, called > RAD3.DataTransformationResult, which will store all results from a series of > preprocessing steps obtained from protocols with type > DataTransformationProtocolType. This will be a simple view with just 5 > relevant attributes: table_id, row_id (pointing to the spot or to the > probeset on the array; a soft link), and float_value/int_value/string_value > (which will be what's now currently stored in RAD3.ProcessResult.value). > > 4. When a series of processing steps is used, we will only store the results > from the *final* step and the corresponding protocol will be of type > "transformation_protocol_series". > > 5. For processes which are simple normalizations of a given quantification > (or of a pair of quantifications for 2-channel data), the input to the > analysis will be a LogicalGroup consisting just of that quantification (resp. > pair of quantifications). For processes which involve averaging across > quantifications the input LogicalGroup will contain 2 or more quantifications > > 6. In terms of plugins, the current AnalysisResultLoader in the GUS/RAD cvs > repository at Sanger will do. (Enhancements or auxiliary plugins might be > written for the specific case in which the analysis is an up-stream (=low > level=processing) one. So this plugin will do the job that the > ProcessResultLoader was doing for the Process tables.) > > Elisabetta > |
