>To: "Khan, Sohail" <khan at="" cshl.edu=""> >From: Naomi Altman <naomi at="" stat.psu.edu=""> >Subject: Re: [BioC] Scaling Factor for Affymetrix chips. >Cc: >Bcc: >X-Eudora-Signature: <work> >Date: Sun, 12 Mar 2006 16:10:37 -0500 > >Personally, usually go straight to the probe level data and do: > >1) image plot of all the arrays >2) pairs plot of all pm probes on all pairs of arrays (preferably >using hexbin) >3) density or histogram of all pm probes on each array >4) RNA degradation plot (looking for parallel lines) > >--Naomi > > >At 11:49 AM 3/12/2006, you wrote: >>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 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >Naomi S. Altman 814-865-3791 (voice) >Associate Professor >Dept. of Statistics 814-863-7114 (fax) >Penn State University 814-865-1348 (Statistics) >University Park, PA 16802-2111 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111