[BioC] problem read.maimage("Agilent") -limma
naomi at stat.psu.edu
Tue Jul 26 16:46:37 CEST 2005
There are "\" and "#" before the offending line. I could not find any
other unusual characters in the offending line.
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
>>>read.maimage in Limma under R 2.1.1 (I don't know the limma version,
>>>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
>>>But under R 2.1.I, I get:
>>>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.
Naomi S. Altman 814-865-3791 (voice)
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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