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