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

[Sean Davis]

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