[BioC] problem read.maimage("Agilent") -limma

[Henrik Bengtsson]

Recently we detected some problems with internal regexpr libraries in R 
v2.1.1. One of the symptoms was that R would crash on Windows, but also 
that the regular expression became corrupt in memory. This was partly 
fixed in the R v2.1.1 patched (2005-07-20). Note that this was 
introduced when the went from R v2.1.0 to v2.1.1, so this might be 
related to your problem.

Cheers

Henrik

Naomi Altman wrote:
> There are "\" and "#" before the offending line.  I could not find any 
> other unusual characters in the offending line.
> 
> --Naomi
> 
> At 09:59 AM 7/26/2005, Sean Davis wrote:
> 
> 
>>On Jul 26, 2005, at 8:13 AM, Gordon K Smyth wrote:
>>
>>
>>>>Date: Mon, 25 Jul 2005 12:22:22 -0400
>>>>From: Naomi Altman <naomi at stat.psu.edu>
>>>>Subject: [BioC] problem read.maimage("Agilent") -limma
>>>>To: bioconductor at stat.math.ethz.ch
>>>>
>>>>I am having trouble reading the Agilent arabidopsis 22575 gene array
>>>>using
>>>>read.maimage in Limma under R 2.1.1 (I don't know the limma version,
>>>>but I
>>>>just downloaded using the R packages interface, and also used the
>>>>update,
>>>>so I presume this is the most recent.
>>>
>>>You should have limma 2.0.2.
>>>
>>>
>>>>Under R 2.0.1, there was no problem reading all the data in the
>>>>arrays using:
>>>>
>>>>RGf=read.maimages(c("2792.txt","2793.txt","2796.txt","4507.txt","4508. 
>>>>txt","4509.txt"),source="agilent"
>>>>)
>>>>
>>>>dim(RGf$R)
>>>>22575     6
>>>>
>>>>
>>>>But under R 2.1.I,  I get:
>>>>
>>>>RGf=read.maimages(c("2792.txt","2793.txt","2796.txt","4507.txt","4508. 
>>>>txt","4509.txt"),source="agilent"
>>>>)
>>>>
>>>>dim(RGf$R)
>>>>12956    6
>>>>
>>>>The last line of RGf$R is all NA.
>>>>
>>>>The problem might be in RGf$genes.  When I try to print any row up to
>>>>the
>>>>last one, everything looks normal.  Trying to print the last row kills
>>>>R.  The annotation for this gene appears to be exceptionally long.
>>
>>I have had problems with Agilent annotation files containing "special"
>>characters that cause similar "termination" of file reading.  I would
>>look at the annotation for quotation marks, single quotes, # symbols
>>(no idea why this seems to affect things), and backslashes.  I
>>typically write a little perl script to "clean" the files.  I'm not
>>sure why this should vary from one version to the next, though.
>>
>>Sean
>>
> 
> 
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Bioinformatics Consulting Center
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
> 
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