[BioC] Scaling Factor for Affymetrix chips

Jacky Pallas j.pallas at cs.ucl.ac.uk
Mon Mar 13 12:23:20 CET 2006

Try the simpleaffy package from Crispin Miller et al. for a graphical
summary of scaling factors, %present calls, background etc. for all .cel
files in an experiment. 


From: "Khan, Sohail" <khan at cshl.edu>
Subject: [BioC] Scaling Factor for  Affymetrix chips.
To: <Bioconductor at stat.math.ethz.ch>
        <C8696843AE995F4EA4CDC3E2B83482A901878FA3 at mailbox02.cshl.edu>
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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.
Dr. Jacky Pallas
Bloomsbury Centre for Bioinformatics
Dept. Computer Science
University College London
Gower Street
London WC1E 6BT

Web:    www.bcb.lon.ac.uk

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