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

[Naomi Altman]

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.

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.




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