[BioC] problem read.maimage("Agilent") -limma
sdavis2 at mail.nih.gov
Tue Jul 26 15:59:31 CEST 2005
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
>> 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
>> 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:
>> 22575 6
>> But under R 2.1.I, I get:
>> 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
>> 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.
More information about the Bioconductor