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. Jacky From: "Khan, Sohail" <khan@cshl.edu> Subject: [BioC] Scaling Factor for Affymetrix chips. To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <c8696843ae995f4ea4cdc3e2b83482a901878fa3 at="" mailbox02.cshl.edu=""> Content-Type: text/plain; charset="iso-8859-1" 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