[BioC] LIMMA -- obtaining values used to calculate lfc

[Sam McInturf [guest]]

Hello everyone,
   I am working on a set of affymetrix arrays, and I am interested in obtaining the A and B values in lfc = log(A/B).  

I wrote several small functions to annotate my topTable outputs, and one of these annotations was the exprs() for each probe, but when comparing the lfc's that topTable output, they are very different than the values that I could calculate with the exprs() values.  So I am then lead to believe that the lfc is calculated by expression values that have been adjusted/better estimated by eBayes() and so on.

So can I take a lfc, A, M, exprs(), et cetera to get the values that the log fold change is directly calculated from?

Sorry if this question has been asked, I have no idea how to describe my problem succinctly.  

Cheers!
Sam McInturf 

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

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