Dear list members, I have an expression array dataset done with Agilent one color array, and I wanted to do QC using arrayQualityMetrics. I read in the raw Agilent data using limma and background correct and normalization was done according to limma User's guide. This works fine and I got an EList object. However it seems arrayQualityMetrics doesn't accept EList as input. Any one has an idea? Thanks in advance! Yong [[alternative HTML version deleted]]

Hi Yong, On Tuesday, December 03, 2013 4:56:11 AM, Yong Li wrote: > Dear list members, > > I have an expression array dataset done with Agilent one color array, and I > wanted to do QC using arrayQualityMetrics. I read in the raw Agilent data > using limma and background correct and normalization was done according to > limma User's guide. This works fine and I got an EList object. However it > seems arrayQualityMetrics doesn't accept EList as input. Any one has an > idea? Your best bet is probably converting the EList object into an ExpressionSet. The simplest way to do so is something like library(Biobase) eset <- ExpressionSet(assayData = assayDataNew(exprs = EList$E)) but you can always add in the other slots (phenoData, featureData, etc) if you so desire. Best, Jim > > Thanks in advance! > > Yong > > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099