Thanks, Jim. That's very helpful. -Jack On Thu, Mar 7, 2013 at 8:57 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Please don't take things off list. > > On 3/6/2013 7:59 PM, Jack Luo wrote: > >> Gene 1.0 ST. >> > > At this point I guess I need to know what you mean by gene level. The affy > package by definition only summarizes at the transcript level. But that > doesn't mean that you only have one probeset per gene, as there may still > be duplicates (splice variants or whatnot). If you just want a single > expression value per gene, you can either use the genefilter package to > subset by Entrez ID, or you could alternatively use one of the MBNI > re-mapped cdf packages. > > Best, > > Jim > > > >> On Wed, Mar 6, 2013 at 2:53 PM, James W. MacDonald <jmacdon@uw.edu<mailto:>> jmacdon@uw.edu>> wrote: >> >> Hi Jack, >> >> >> On 3/6/2013 11:48 AM, Jack Luo wrote: >> >> Hi, >> >> I am trying to RMA normalize a bunch of cel files and output >> the gene >> >> >> A bunch of cel files of what Array type? >> >> >> expression matrix to gene level (instead of probe set level), >> is there any >> option in justRMA that can do this (or any other function that >> can do >> this?) I searched the options on justRMA, does not seem to >> have this >> option. >> >> Thanks, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: >> http://news.gmane.org/gmane.**science.biology.informatics.** >> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]