Hi Patrick, Thanks a lot for the quick reply. I updated the package and it didn't fix the error. c On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote: > Charlie, > I don't know if this is related to you issue, but a bug in the gcrma > package was just fixed and there is a version 2.14.1 is now up on > bioconductor.org. Update to the latest version of gcrma and see if > it addresses your issue. > > > Patrick > > > > charliew wrote: >> Dear List, >> I've encountered the following error when running LPE: >> >> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >> mean(var.M.adap[i + : >> replacement has length zero >> >> It happens when the CEL files have been processed with gcRMA but >> not when they have been processed with RMA. >> I'm not positive about this but I think this error first started >> happening with the upgrade to gcRMA 2.x >> I think it is happening because gcRMA is producing a lot of probes >> with identical expression values. >> >> Here is a test session that causes the error. Upon request I can >> provide a tarball of the test data but any collection of CEL files >> will reproduce the error. >> The error also occurs if you run gcRMA from within onecolorGUI or >> affylmGUI. >> It also happens if you first write the expression data to a file >> with write.exprs, then read it back in with read.table. >> >> #Loading the packages >> > library(affy) >> Loading required package: Biobase >> Loading required package: tools >> >> > library(gcrma) >> Loading required package: matchprobes >> Loading required package: splines >> >> > library(LPE) >> > set.seed(0) >> >> #Reading in 4 CEL files >> > test.Dat<-ReadAffy() >> >> #Summarizing with gcRMA >> > test.gcrma<-gcrma(test.Dat) >> Adjusting for non-specific binding....Done. >> Normalizing >> Calculating Expression >> >> #Summarizing with RMA >> > test.rma<-rma(test.Dat) >> Background correcting >> Normalizing >> Calculating Expression >> >> #Extracting gcRMA assay data >> > test.gcrma.MAT<-exprs(test.gcrma) >> > dim(test.gcrma.MAT) >> [1] 15611 4 >> >> #Extracting RMA assay data >> >> > test.rma.MAT<-exprs(test.rma) >> > dim(test.rma.MAT) >> [1] 15611 4 >> >> #Running LPE function on gcRMA data and the resulting error >> > var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01) >> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), >> mean(var.M.adap[i + : >> replacement has length zero >> >> #Running LPE function on RMA data - it successfully completes >> > var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01) >> > >> >> #My session info >> > sessionInfo() >> R version 2.8.0 (2008-10-20) >> i386-apple-darwin8.11.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0 >> LPE_1.16.0 gcrma_2.14.0 >> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.10.0 preprocessCore_1.4.0 >> >> Thanks a lot for your help >> >> Charlie >> >> ------------------------------------------------------------------- --------- >> Charlie Whittaker, Ph.D. >> Bioinformatics and Computing Core Facility >> The David H. Koch Institute for Integrative Cancer Research At MIT >> 77 Mass Ave E18-366 >> Cambridge, MA 02139 >> >> 617-324-0337 >> >> _______________________________________________ >> 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 >