hii... this is Deepak.... i am working on analysis of microarray data using bioconductor and i am rank amateur in R I tried using this code snippet phenoData(spikein95) <- new("phenoData", pData = pd, varLabels = vl) but it said that phenoData is now defunct and we need to use AnnotatedDataFrame. And i am not able to proceed because of the following error AnnotatedDataFrame(x1)<-new("AnnotatedDataFrame",pData=pd, varLabels=v1) Error in .nextMethod(.Object, ...) : invalid names for slots of class “AnnotatedDataFrame”: pData, varLabels i am basically trying to segregate the samples into 3 parts containing normal, HSIL and SCC data and this is the code that i have used till now... setwd("E:\\Project\\CEL files\\Old\\GSE7803-3") > f1=list.celfiles(path="E:\\Project\\CEL files\\Old\\GSE7803-3") > x1<-ReadAffy(filenames=f1) > pd <- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2, + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3), + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,4,5,6,7, + 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21)) > rownames(pd) <- sampleNames(x1) > v1 <- list(population = "1 is normal, 2 is HSIL, 3 is SCC", replicate="arbitary numbering") i further wish to perform rma and then generate a MA plot. kindly help me rectify this error and please explain with an *example* so that i could proceed further. [[alternative HTML version deleted]]