Hi All, I just noticed that justGCRMA in Bioconductor 2.5 output identical intensities across all samples for a subset of probesets on HGU133plus2 chip. I used the command: > data <- justGCRMA() I've seen it on a couple datasets - one run on linux, one on a PC. The dataset run on linux is in GEO (GSE9843). I haven't looked carefully but it seems to occur for some of the lower-intensity probesets. I wonder is this a bug? Thanks, Brian [[alternative HTML version deleted]]

Hi Brian, Brian_Hare at vrtx.com wrote: > Hi All, > > I just noticed that justGCRMA in Bioconductor 2.5 output identical > intensities across all samples for a subset of probesets on HGU133plus2 > chip. I used the command: > >> data <- justGCRMA() > > I've seen it on a couple datasets - one run on linux, one on a PC. The > dataset run on linux is in GEO (GSE9843). I haven't looked carefully but > it seems to occur for some of the lower-intensity probesets. > > I wonder is this a bug? No, but it _is_ documented in the mailing list archives: http://article.gmane.org/gmane.science.biology.informatics.conductor/5 665/match=gcrma > suppressMessages(library(gcrma) > eset <- justGCRMA() Computing affinitiesLoading required package: AnnotationDbi .Done. Adjusting for optical effect.............Done. Adjusting for non-specific binding............Done. Normalizing Calculating Expression > a <- apply(exprs(eset), 1, var) > sum(a == 0) [1] 693 > eset2 <- justGCRMA(fast=F) Computing affinities.Done. Adjusting for optical effect.............Done. Adjusting for non-specific binding............Done. Normalizing Calculating Expression > b <- apply(exprs(eset2),1,var) > sum(b == 0) [1] 0 Best, Jim > > > Thanks, > > Brian > > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues