Dear users,
 
           I often encounter memory problems when I use rma or gcrma to
analyze Affymetrix genechip data (i.e. hgu133atag,  22300 genes and 42
arrays). For memory problem, someone suggest to separate all arrays into
several parts, apply rma or gcrma to these parts and then combine the
results. Because rma and gcrma apply median polish algorithm, and median
polish is quite sensitive with the number of arrays. I don't think the
combined result can be consistent with the result using all arrays. 
 
           > Data<-ReadAffy( )
After reading all CEL files using ReadAffy, if AffyBatch object (Data)
can be separated into several small objects in terms of genes, and then
use rma or gcrma to analyze these projects. I think this combined result
should be consistent with the results using all arrays. I know
split.AffyBatch can split AffyBatch, but I don't know is it possible to
split AffyBatch project in terms of genes? Anyone knows how to do that? 
           
 
Regards & Thanks
 
Chen
 
 

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