Hi, 
  I have about 53 cel files, each one has the size of about 12-13 mega bytes with 22625 probes. I am using affycoretools to do rma, but it complains that the maximum size of memory has been reached. My PC is Windows XP with 2G RAM. Below is the error information. 

Error: cannot allocate vector of size 209906 Kb
In addition: Warning messages:
1: Incompatible phenoData object. Created a new one.
 in: read.affybatch(filenames = filenames, phenoData = phenoData) 
2: Reached total allocation of 1024Mb: see help(memory.size) 
3: Reached total allocation of 1024Mb: see help(memory.size) 

Since RMA is an across sample normalization, and I need to analyze all the 53 samples together, I can not separate them into several pieces and then do RMA, MAS5 can do that, but the expression value obtained by MAS5 is not as good as that of RMA. Does anybody know how to solve this problem? In addition, it seems that the output of rma in affy package (not affycoretools) has several lines for each individual probe (my case is 11 lines for each individual probe), while the rma in affycoretools directly gives the final expression value for each probe, could anybody tell me how to make the two results from affy and affycoretools comparable with each other? 

Thanks a lot!

James

 
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