[BioC] problem read.maimage("Agilent") -limma
Gordon K Smyth
smyth at wehi.EDU.AU
Tue Jul 26 14:13:02 CEST 2005
> 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:
> 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 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've just tried reading in some AgilentFE data and didn't have any problems. So I wasn't able to
reproduce the error that you describe.
Try isolating which input file is causing the problem. If you don't find a solution, you could
zip up an example data file which causes the error and send it to me.
> 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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