HI list, how are people normalizing 133a and b chips? here is what I am doing. 1) bg.correct.rma2 (so this is per chip) 2) extract the pm values for all chips 3) for each pair (A and B) get the probes in common (168 genes) and make a linear correction factor to to correct the B chip. 4) adjust all the B chips to thir corresponding A chip 5) put the data (A and B) in a matrix and do quantile normalization 6) this gives me the corrected probes, unfortunately some are now negative so I add a slight fudge factor 7) I read the probes back into an AffyBatch object and get expression values (medianpolish) does this sound reasonable? bye rob -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://matilda.vu.edu.au/~dunne Email: Rob.Dunne@csiro.au Java has certainly revolutionized marketing and litigation.

Message: 7 Date: Thu, 6 Nov 2003 12:18:14 +1100 From: Rob Dunne <rob.dunne@csiro.au> Hi Rob, I think it's unnecessary and even unadvisable to adjust B to the A chips (your step 3 & 4). The affy package does a good job of normalizing both. Do you find consistent discrepancies between results from A and B chips? regards Mark Subject: [BioC] normalizing 133 a and b To: bioconductor@stat.math.ethz.ch Message-ID: <16297.41302.579995.483402@pride.nsw.cmis.CSIRO.AU> Content-Type: text/plain; charset=us-ascii HI list, how are people normalizing 133a and b chips? here is what I am doing. 1) bg.correct.rma2 (so this is per chip) 2) extract the pm values for all chips 3) for each pair (A and B) get the probes in common (168 genes) and make a linear correction factor to to correct the B chip. 4) adjust all the B chips to thir corresponding A chip 5) put the data (A and B) in a matrix and do quantile normalization 6) this gives me the corrected probes, unfortunately some are now negative so I add a slight fudge factor 7) I read the probes back into an AffyBatch object and get expression values (medianpolish) does this sound reasonable? bye rob -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://matilda.vu.edu.au/~dunne Email: Rob.Dunne@csiro.au Java has certainly revolutionized marketing and litigation. -- Mark Reimers, Assistant Professor, Department of Biosciences, and Statistical Expert, Expression Analysis Facility, Karolinska Institute phone: +46-8-608-3333; http://www.bea.ki.se/staff/reimers/