hello, i was following the discussion about "vsn on log" array data. does it apply also for the RMA-preprocessed affy data? since the expression values are log-scaled, is it incorrect to perform vsn normalization on them? thanks d -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm

Hi Dario, > i was following the discussion about "vsn on log" array data. > does it apply also for the RMA-preprocessed affy data? > since the expression values are log-scaled, is it incorrect to > perform vsn normalization on them? Yes, it is incorrect. It is also not necessary, because RMA does a background correction that is (for the data I've seen) in fact quite close to "variance stabilization". Please see the vignette of vsn for an example of how to use vsn as a normalization method for Affymetrix data: http://www.bioconductor.org/repository/devel/vignette/vsn.pdf (Section 3 on page 8) library("affy") library("vsn") result = expresso(myAffyBatch, bg.correct = FALSE, normalize.method = "vsn", pmcorrect.method = "pmonly", summary.method = "medianpolish") Cheers Wolfgang -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber