[BioC] How to analyze Affy data, CEL files not available

[Bobby Prill]

I would like to analyze a set of 40 Affy experiments, but I do not  
have the CEL files.  What I have is a spreadsheet of the MAS  
expression measures, one column per array.  Each row corresponds to  
one gene.

I load the data:
eset = read.exprSet(exprs="mydata.txt", phenoData="phenoData.txt")

My general question is, should/can I perform some sort of  
normalization so that the arrays are comparable from one to  
another?   or is this what MAS has already done?  (I'm not familiar  
with Affy MAS.)

Other problems include:

1. MA plots indicate that the data cloud is skewed (not perfectly  
centered on M==0 line).  Should I loess?

2.  Also, the M values have high variance at low A, which I think is  
a byproduct of the MAS. Probably nothing I can do about this.

I think the typical advice would be to obtain CEL files and run rma 
().  But if I'm stuck with the MAS expression calls, what to do?

Thanks.

- Bobby