Hello list, Im having a rather strange issue here. I have a set of microarray samples (226) collected from GEO from different studies on the same platform (pd.mogene.1.0.st.v1). My intention is to read CEL files all together and then divide the GeneFeatureSet in smaller objects corresponding to the different studies. Somehow though, im able to do that only in linux environment with R 3.0.0 while if i try on windows with R 3.0.2 it throws me the following error when i try to subset the GeneFeatureSet object: library(oligo) pd<- read.table("pd.txt", header=T) rownames(pd)<- pd$EXACT_CEL_FILES RawData<- read.celfiles(rownames(pd)) pda<- as(pd, "AnnotatedDataFrame") phenoData(RawData)<- pda studiesID<- levels(RawData$Study) for(i in 1:length(studiesID)){ d<-studiesID[i] assign(d, RawData[,pData(RawData)$Study == studiesID[i]]) } Error in `$<-.data.frame`(`*tmp*`, "channel", value = integer(0)) : replacement has 0 rows, data has 7 I attach both the sessionInfo for Linux and Windows. Thank you very much! -- output of sessionInfo(): > sessionInfo() [LINUX] R version 3.0.0 (2013-04-03) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.4 [3] DBI_0.2-7 oligo_1.24.2 [5] Biobase_2.20.1 oligoClasses_1.22.0 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 BiocInstaller_1.10.4 [4] Biostrings_2.28.0 bit_1.1-12 codetools_0.2-8 [7] ff_2.2-13 foreach_1.4.2 GenomicRanges_1.12.5 [10] IRanges_1.18.3 iterators_1.0.7 preprocessCore_1.22.0 [13] splines_3.0.0 stats4_3.0.0 tools_3.0.0 [16] zlibbioc_1.6.0 > sessionInfo() [WINDOWS] R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mogene.1.0.st.v1_3.8.0 RSQLite_0.11.4 DBI_0.2-7 oligo_1.26.6 Biostrings_2.30.1 [6] XVector_0.2.0 IRanges_1.20.7 Biobase_2.22.0 oligoClasses_1.24.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] affxparser_1.34.2 affyio_1.30.0 BiocInstaller_1.12.1 bit_1.1-12 codetools_0.2-8 ff_2.2-13 [7] foreach_1.4.2 GenomicRanges_1.14.4 iterators_1.0.7 preprocessCore_1.24.0 splines_3.0.2 stats4_3.0.2 [13] tools_3.0.2 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.