Hi all- I have been doing our microarray analysis looking at the QC metrics provided by SimpleAffy and releazed that all the data produced is based on the MAS5.0 algorithm. I was wondering if there was any way to get qc metrics if use RMA or GCRMA, specifically we want to know about the background values. I have been combing through the vignettes and postings and cannot locate anything. Any help would be appreciated. Thanks Louisa "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu

Dear Louisa have a look at the "arrayQualityMetrics" package. Can you explain what you mean by "we want to know about the background values"? Best wishes Wolfgang 21/08/2008 17:10 Louisa A Rispoli/AS/EXP/UTIA scripsit > Hi all- > > I have been doing our microarray analysis looking at the QC metrics > provided by SimpleAffy and releazed that all the data produced is based on > the MAS5.0 algorithm. I was wondering if there was any way to get qc > metrics if use RMA or GCRMA, specifically we want to know about the > background values. I have been combing through the vignettes and postings > and cannot locate anything. Any help would be appreciated. > > Thanks > > Louisa > > "If we knew what we were doing, it wouldn't be called Research." - Albert > Einstein > > Louisa Rispoli, Ph.D. Reproductive Physiology > Department of Animal Science > University of Tennessee, Knoxville > A105 Johnson Animal Research and Teaching Unit > 1750 Alcoa Highway > Knoxville, TN 37920 > phone:(865) 946-1874 > fax:(865) 946-1010 > email: lrispoli at utk.edu >