[BioC] Scaling Factor for Affymetrix chips.

[Khan, Sohail]

Dear All,

Is the Scaling Factor (from GCOS) still neccessary for the quality assessment of Affy, eventhough we are applying RMA or GCRMA for the probe level analysis??  Many times we only have the .cel files from an experiment, in this case how can one have a look at the SF using any BioC package?  Could you recommend a comprehensive QC method/procedure for the Affymetrix chip? Thanks.

Sohail Khan 
Scientific Programmer 
COLD SPRING HARBOR LABORATORY 
Genome Research Center 
500 Sunnyside Boulevard 
Woodbury, NY 11797 
(516)422-4076