[BioC] Farms library

phguardiol at aol.com phguardiol at aol.com
Fri Jun 16 21:09:34 CEST 2006

I ve been trying the new FARMS library to analyse primary signals of 
Affy U133A chips (using R2.4dev downloaded yesterday on a PC with 
winXPPro) which according to a recent publication in Bioinformatics is 
more accurate than RMA / gcRMA etc...

Why is it that I get for more than 3/4 of the probesets the same signal 
values for all chips for a given probesets ? and this in multiple 
different set of chips. Such as probeset1 gave for chip1, 2, 3, etc... 
the same intensity values for all chips ??? Is it because of the 
normalisation process proposed here ? I m septic...

BTW, I used the q.farms function there in such a way:
data1 <- ReadAffy()
data2 <- q.farms(data1)

thank for the help
Philippe Guardiola, MD

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