[BioC] rmaPLM vs fitPLM

[Ariel Chernomoretz]

Dear list,

I obtain different values for chip effects
using fitPLM or rmaPLM: 
 
>Pset<-fitPLM(Data,model=PM~-1+probes+samples,output.param=list(weights=TRUE)) 
>Pset.rma <-rmaPLM(Data,output.param=list(weights=TRUE))

I did not expect that as I thought that, by default, both procedure use the 
same bkg+normalization+summarization 

Any help will be welcome
Regards,

Linux AMD Opteron 64bit 
R Version 2.0.1 
affyPLM 1.2.5
affy1.5.8


Ariel./


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