[BioC] problems with affy in unix

[fwan]

Thanks, Dr. James:

For the 2nd question, The ReadAffy did go wrong. I tried justRMA on the same
cel files of class BCR and there are sample names instead of just "H".
samples names are cel file names.

for the 3rd question, I still need some help. I have 335 cel files in total
and I even tried justRMA and it always went wrong when it read in the 127th
file, saying something like:
could not open Hyperdip-5-C.cel (it is not problem with this cel file, i
deleted it and justRMA went wrong again at another 127th file with same
error message). My question is: if I break 335 into 3 groups ( approximately
110 cel files in a group and each group contains a few classes of lukemia
cel files defined by saint jude childrens. there are 9 classes:
BCR,NORMAL,HYPERDODIP,MLL..etc) and then run justRMA on each group and merge
the final expression files later, is this process justified for the later
data analysis ? I know this expression file will be different from the
expression file i can get from justRMA on 335 cel files at one time.
however, upgrading the mainframe might not be possible right now.

thanks again for your help. good weekend.

regards,

w.f