
Hi all,
I have some raw data as well as Affymetrix MAS5 normalized data for oligonucleotide arrays.
For the raw data I use the mas5 function of the affy package.
>From then on I run the same code on both (removing AFFY controls, applying log, selecting genes over a certain fold change etc.).
I end up with different numbers of genes...
I have done A LOT of debugging (including doing the same actions manually in excel :o/ ) and am quite convinced now that the difference has to do with the normalization itself.
The values of normalized data are very different, with the R normalized data having much higher values.
I noticed that the mas5 function in the Affy package uses 500 as a scaling value. 
Can that be the source of the difference I see?
Is there anyway to better approximate the MAS5 scaling?
Thanks!
Liat. 		 	   		  
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