
Hi-
I am in the process of analyzing affymetrix data for prostate cancer patients. I have generated expression data with the RMA function and need to do a pairwise comparison. Can someone please help as to what this error means:

results <- pairwise.comparison(x.rma, "Phenotype", c("normal", "cancerous"), raw.data)

Error in fastT(cbind(a.samples, b.samples), 1:ai, (ai + 1):(ai + bi),  : 
  wrong sets of columns


Thanks!
 		 	   		  
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