[GeneX-dev] Re: Data with negative numbers...

[Harry M. <man...@ho...>]

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.
> >