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

[Naomi Altman]

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