[BioC] problem reading genepix files using both marray andlimma functions

[Gordon Smyth]

Dear Bela,

Thank you for sending me three of your gpr files. As Mick Watson has 
already written to you offline, your gpr files contain a lot of problems 
and have clearly been edited (mutilated) in some way after being output by 
GenePix.

1. You have instances where the tab separating two numbers has been deleted 
resulting in nonsense strings such as "0.3440.041".

2. In the file "L12797021.gpr" there is a very serious problem where 7 
lines, apparently from the end of the file, have been moved and inserted 
starting line 50992. Attached to this chunk of lines is a sequence of 371 
null characters. These are not ascii characters and should never appear in 
a GAL file. They are interpreted by R as end-of-file and produce premature 
termination of reading the file.

Errors such as those above are your responsibility and not that of 
Bioconductor package authors.

3. Even more importantly, all three gpr files that you sent me were 
produced using different GAL files:

 > files
[1] "A12797013.gpr" "H12801606.gpr" "L12797021.gpr"
 > readGPRHeader(files[1])$GalFile
[1] "E:\\GALfilevrs2.gal"
 > readGPRHeader(files[2])$GalFile
[1] "D:\\TimWilkes\\24-6-4 No.1 G final.gal"
 > readGPRHeader(files[3])$GalFile
[1] "D:\\TimWilkes\\CSS5SRLday3\\2-7-4 k final.gal"

Different GAL files mean that the probes may differ between arrays or that 
the same probes may be different locations. Both read.maimages() and 
read.GenePix() are designed to read batches of arrays all corresponding to 
the same GAL file. You cannot expect to read in data from different GAL 
files at one time.

At 12:16 AM 18/08/2004, Bela Tiwari wrote:
>Hello,
>
>Thanks for the responses about my email and the offers of help.
>
>I have now upgraded to the latest version of limma from the wehi site.
>I also wrote to the person who provided the gpr files I have, and she
>says they have not been touched/edited, etc. She copied new versions of
>the files for me from a CD she burned when she first received the files,
>and these are identical to the ones I have been using. (Same sizes, same
>errors.)
>
>I tried to load all the gpr files as before, using read.maimages. This
>caused problems again, though the error message may be a bit more
>telling this time perhaps (see below).
>
>I then tried loading just those files that  I had been able to load
>individually without errors using the older version of read.maimages. -
>this worked! Hurrah!  At least that's now a total of 8 of my files (of a
>total of 16) that I can now load without problem.
>
>Here is the error message that appeared when attempting to load all
>files:
>
> > mynewLimmaData <-read.maimages(gprfiles, source = "genepix")
>Read A12797013.gpr
>Error in "[<-"(`*tmp*`, , i, value = as.integer(c(53, 46, 49, 227, 57,
>:
>         number of items to replace is not a multiple of replacement
>length
>
>Given this, I hope you don't mind if I take up your offer and end you a
>couple of the gpr files (offlist). I hope you can spot the errors that I
>am missing.
>
>I should, of course, have remembered to find out what version of limma I
>was already using before I upgraded....oh well. I am pretty sure (from
>another machine like mine), that this is the correct version info for
>both R and limma:
> >version
>platform i686-pc-linux-gnu
>arch     i686
>os       linux-gnu
>system   i686, linux-gnu
>status
>major    1
>minor    9.0
>year     2004
>month    04
>day      12
>language R
>
> > packageDescription("limma")
>Package: limma
>Version: 1.6.7
>Date: 2004/05/14
>Title: Linear Models for Microarray Data
>Author: Gordon Smyth <smyth at wehi.edu.au>, Matt Ritchie
>         <mritchie at wehi.edu.au>, James Wettenhall
>         <wettenhall at wehi.edu.au>, Natalie Thorne <thorne at wehi.edu.au>
>Maintainer: Gordon Smyth <smyth at wehi.edu.au>
>Depends: R (>= 1.7.1), MASS, splines, statmod (>= 1.0.6), sma
>Description: Data analysis, linear models and differential expression
>         for microarray data.
>License: LGPL
>URL: http://bioinf.wehi.edu.au/limma/
>Packaged: Wed May 26 14:31:46 2004; madman
>Built: R 1.9.0; ; 2004-07-27 16:54:06; unix

I had intended that you would run packageDescription() *after* upgrading so 
that we could confirm that you were indeed using the latest version of the 
software.

Gordon

>cheers,
>
>Bela
>
>
>*************************
>Dr. Bela Tiwari
>Lead Bioinformatician
>
>CEH Oxford
>Mansfield Road
>Oxford, OX1 3SR
>01865 281975
>
>*************************