Hi list, I'm trying to download GSE11595. It throws an error (see below) when I try to download as GSEMatrix=TRUE, but runs through with tons of warnings under the GSEMatrix=FALSE parameter. R is up-to-date, a clean install (sessionInfo below). Is there a way to fix the download as GSEMatrix=TRUE, as I prefer the resulting data structure? Many thanks, Hendrik > GSE11595<-getGEO("GSE11595",GSEMatrix=TRUE) Found 2 file(s) GSE11595-GPL3906_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE11595/GSE11595-GP L3906_series_matrix.txt.gz' ftp data connection made, file length 59641 bytes opened URL downloaded 58 Kb Error in `rownames<-`(`*tmp*`, value = c(2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, : attempt to set rownames on object with no dimensions > sessionInfo() R version 2.14.2 (2012-02-29) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.21.9 Biobase_2.14.0 loaded via a namespace (and not attached): [1] RCurl_1.91-1.1 XML_3.9-4.1 -- Dr. Hendrik Falk Senior Research Officer High Throughput Chemical Screening Facility The Walter and Eliza Hall Institute of Medical Research Biotechnology Centre 4 Research Avenue Bundoora Victoria 3086 Australia Tel. (+61 3) 9345 2104 Fax. - 2211 Mob. 0420 353572 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}

On Thu, Mar 29, 2012 at 1:59 AM, Hendrik Falk <falk at="" wehi.edu.au=""> wrote: > Hi list, > > I'm trying to download GSE11595. It throws an error (see below) when I try to > download as GSEMatrix=TRUE, but runs through with tons of warnings under the > GSEMatrix=FALSE parameter. R is up-to-date, a clean install (sessionInfo below). > > Is there a way to fix the download as GSEMatrix=TRUE, as I prefer the resulting data > structure? Thanks, Hendrik. This should be fixed in SVN and will propagate to the build system in the next day or so. Sean