here is the code for the issue I am having. Thanks again for you help > > length(pm(data[,1])) [1] 120855 > > > #############remove selected S. cerevisiae probe Ids > > > > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > ResetEnvir(cleancdf) Loading required package: yeast2cdf Loading required package: yeast2probe > > RemoveProbes(listOutProbes[1:233],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[233:467],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[467:500],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[500:600],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[600:640],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[640:650],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[650:700],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[700:710],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[710:720],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[720:800],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[800:884],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 119991 > >######listOutProbes is a character vector of probe ID's. I don't know why I had to subset it like this, putting the >######whole vector in, or larger subsets gave; >######> RemoveProbes(listOutProbes,listOutProbeSets=NULL, cleancdf) ####### Error in ans[[i]][, i.probes] : incorrect number of dimensions > > > > > >############remove s. pombe probesets > > > > s_cerevisiae<-scan("s_cerevisiae.msk", skip=2, list("", "")) Read 5028 records > pombe_filter_out<-s_cerevisiae[[1]] #the probesets you DONT want. > > > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > RemoveProbes(listOutProbes=NULL, pombe_filter_out, cleancdf) > length(pm(data[,1])) [1] 64688 ? > >#################################read in the new data and do the RMA > > > pd<-read.AnnotatedDataFrame("targets.txt",header=TRUE,row.names=1,as .is=TRUE) # reads the names from the targets file > data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) # reads all .CEL files in the working directory and assigns them names from the target files > > eset <- rma(data)#does the normalisation Background correcting Normalizing Calculating Expression Error in rma(data) : length of 'dimnames' [1] not equal to array extent > > > > > traceback() 2: .Call("rma_c_complete", pm(object, subset), pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 1: rma(data) > > > > > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] yeast2probe_2.3.0 yeast2cdf_2.3.0 matchprobes_1.14.0 [4] yeast2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [7] AnnotationDbi_1.4.2 affy_1.20.0 Biobase_2.2.1 [10] limma_2.16.3 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0 > Omri Yahel On Thu, Dec 18, 2008 at 4:04 AM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Omri, > > I'm assuming that the RemoveProbes.r function is the one I have posted to > the Bioconductor mailing list several times, mostly recently with some > changes on Sept 24, 2008? > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > If so, would you post your entire session, including the code you used to > remove the probe sets and probes, along with your sessionInfo()? That should > give us more details so we can help you. > > Thanks, > Jenny > > > At 10:08 PM 12/16/2008, Omri Yahel wrote: > >> Hello >> >> I am encountering an error during RMA of an affybatch. >> I have used RemoveProbes.r to remove all S. pombe probesets and 864 >> individual S.cerevisiae probes from the yeast2 platform. >> >> >data<-ReadAffy() >> > data >> AffyBatch object >> size of arrays=496x496 features (11 kb) >> cdf=Yeast_2 (5900 affyids) >> number of samples=26 >> number of genes=5900 >> annotation=yeast2 >> notes= >> > >> > length(pm(data[,1])) >> [1] 64688 >> >> >> When I attempt to compute the eset >> >> > eset <- rma(data) >> Background correcting >> Normalizing >> Calculating Expression >> Error in rma(data) : length of 'dimnames' [1] not equal to array extent >> >> I assume this has something to do with the removal of individual probes >> from >> the environment, but am not sure and do not know how to remedy this. >> Any help appreciated >> >> Omri Yahel >> MSc student >> School of Biological Sciences >> University of Auckland, New Zealand >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]