Dear All: I tried to use nsFilter but keeps getting this error: Error in rows[i] : invalid subscript type 'list' I do not know what went wrong, please help... -- output of sessionInfo(): my code: exprs <- read.table("cia-filtered-dataframe.txt", header=TRUE, sep="\t", row.names=1, as.is=TRUE) exprx<-as.matrix(exprs) pData <- read.table("cia-phenodata.txt",row.names=1, header=T,sep="\t", as.is=TRUE) phenoData <- new("AnnotatedDataFrame",data=pData) annotation <- "mouse4302.db" cia <- ExpressionSet(assayData=exprx,phenoData=phenoData,annotation="m ouse4302.db") library(genefilter) filtered_eset <- nsFilter(cia, require.entrez=TRUE, remove.dupEntrez=TRUE, var.func=IQR, var.filter=FALSE, var.cutoff=0.25, filterByQuantile=TRUE, feature.exclude="^AFFX") -- Sent via the guest posting facility at bioconductor.org.