Dear Som, Of course you can use FARMS with alternative CDFs. We always use it in that way. Because of the increase in performance it has made even its way into the standard processing pipelines of some pharma companies! Here is an example for the HuGene11stv1 array: install either these packages (Linux) http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezgcdf_15.0.0.tar.gz http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezgprobe_15.0.0.tar.gz http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezg.db_15.0.0.tar.gz or these packages (Windows) http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezgcdf_15.0.0.zip http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezgprobe_15.0.0.zip http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15. 0.0/entrezg.download/hugene11stv1hsentrezg.db_15.0.0.zip specify at reading in: require(affy) require(farms) rawdata <- ReadAffy(filenames=list.files(), cdfname="hugene11stv1hsentrezg") expressionData <- qFarms(rawdata) specify cdf later: require(affy) require(farms) rawdata <- ReadAffy(filenames=list.files()) rawdata at cdfName <- "hugene11stv1hsentrezg" annotation(rawdata) <- "hugene11stv1hsentrezg" expressionData <- qFarms(rawdata) Regards, G?nter Klambauer On 07/30/2012 09:56 AM, hochreit wrote: > > > > > ---------- Forwarded message ---------- > From: "hochreit" <hochreit at="" bioinf.jku.at=""> > To: "okko clevert" <okko at="" clevert.de="">, "andi mitterecker" > <mitterecker at="" bioinf.jku.at=""> > Subject: [BioC] FARMS package (fwd) > Date: Thu, 19 Jul 2012 15:15:51 +0200 > > > > ---------- Forwarded message ---------- > Message-ID: <snt108-w5716db1d77cb762acbb689cdd90 at="" phx.gbl=""> > From: somnath bandyopadhyay <genome1976 at="" hotmail.com=""> > To: <bioconductor at="" r-project.org=""> > Date: Thu, 19 Jul 2012 06:14:28 -0400 > Subject: [BioC] FARMS package > > Hi, > I was wondering if there is a way of using alternative CDF > (brainarray) and PLIER normalization in the FARMS (Factor Analysis for > Robust Microarray Summarization) package. I want to further use the > I/NI filter to retain informative probesets. Any help would be > appreciated. > Thanks,Som. > [[alternative HTML version deleted]] > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor