Kamila vsnrma (in the vsn package) might be an option for you to try that provides the same probe summary as "normal" rma, but a less aggressive between-array normalisation (namely, only a shifting and scaling, i.e. affine-linear). See also Deepayan Sarkar et al. in NAR 2009, "Quality Assessment and Data Analysis for microRNA Expression Arrays", http://nar.oxfordjournals.org/cgi/content/full/37/2/e17 In addition, if you have "negative controls", i.e. probes on the array for which you are willing to believe that they most of them don't change expression, then you can fit the shifting and scaling factors on these, and then apply to all probes. Best wishes Wolfgang On Jul/11/10 5:11 PM, Steve Shen wrote: > Will affymetrix qc tool wook? > http://www.affymetrix.com/estore/partners_programs/programs/develope r/tools/devnettools.affx#miRNAQC > > steve > > On Sat, Jul 10, 2010 at 11:26 AM, Kamila Naxerova > <naxerova at="" fas.harvard.edu="">wrote: > >> Dear list, >> >> I was searching the archives for discussions about the Affymetrix miRNA >> chip... there are only a few threads and most of them are almost a year >> old. I was wondering whether in the meantime people had gathered some >> experience with analysis strategies - normalization in particular - and were >> willing to share some insights. I do not feel comfortable using RMA because >> I doubt that total miRNA expression can be assumed to be constant across >> samples (particularly when studying developmental processes or cancer). Has >> anybody played with the options? >> >> Thanks! >> Kamila >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber