Hello I have four groups a 5 chips each, all Affymetrix chips. I would like to be able to normalize them separately (within-group) and then see the scaling factor between them. I have now got so far that I have four normalized affybatch objects. > class(mockbgnorm) [1] "AffyBatch" attr(,"package") [1] "affy" > and three more like this one. I was reading the normalize.AffyBatch.constant docs, and I gather that if I can make an affybatch object containing for instance all of mockbgnorm and one chip from the set I am comparing with, I can do normalize.AffyBatch.constant with the comparison chip as the reference. However, I am stuck at making this affybatch object. Can anyone give me any tips on how to best do this? Am I thinking correctly? Thanks, Karin -- Karin Lagesen, PhD student karin.lagesen at medisin.uio.no http://folk.uio.no/karinlag

Hi Karin, Karin Lagesen wrote: > Hello > > I have four groups a 5 chips each, all Affymetrix chips. I would like > to be able to normalize them separately (within-group) and then see > the scaling factor between them. Are you trying to scale-normalize your four AffyBatches, or are you trying to figure out what the scaling factor would be? > > I have now got so far that I have four normalized affybatch objects. > > >>class(mockbgnorm) > > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > > and three more like this one. > > I was reading the normalize.AffyBatch.constant docs, and I gather that > if I can make an affybatch object containing for instance all of > mockbgnorm and one chip from the set I am comparing with, I can do > normalize.AffyBatch.constant with the comparison chip as the > reference. However, I am stuck at making this affybatch object. > > Can anyone give me any tips on how to best do this? Am I thinking > correctly? If you are trying to scale things I don't think you really need to mess around with making different AffyBatches. You can simply get the mean or median of the AffyBatch or chip you are trying to scale to and then use that to scale the AffyBatch you are trying to normalize. Best, Jim > > Thanks, > > Karin -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.