[BioC] problem with GDS2eSet function in GEOquery package
Laurent Pays [guest]
guest at bioconductor.org
Thu Feb 7 17:52:35 CET 2013
This is the code I used:
gse <- getGEO(filename='GSE19380_family.soft') with the "GSE19380_family.soft" downloaded on my computer.
Then
GDS2eSet(gse, do.log2=FALSE,GPL=NULL,AnnotGPL=TRUE)
And I receive this error:
Error in getGEO(Meta(GDS)$platform, AnnotGPL = AnnotGPL) :
You must supply either a filename of a GEO file or a GEO accession
Any help would be appreciated
Thanks in advance
-- output of sessionInfo():
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.24.1 CellMix_1.1 GSEABase_1.20.1 graph_1.36.1
[5] annotate_1.36.0 AnnotationDbi_1.20.3 stringr_0.6.2 Rcpp_0.10.2
[9] NMF_0.10.1 Biobase_2.18.0 BiocGenerics_0.4.0 bigmemory_4.3.0
[13] bigmemory.sri_0.1.2 digest_0.6.2 registry_0.2 rngtools_1.1
[17] pkgmaker_0.10.1
loaded via a namespace (and not attached):
[1] beeswarm_0.1.5 codetools_0.2-8 colorspace_1.2-1
[4] corpcor_1.6.4 csSAM_1.2.1 DBI_0.2-5
[7] doParallel_1.0.1 foreach_1.4.0 genefilter_1.40.0
[10] gridBase_0.4-6 gtools_2.7.0 IRanges_1.16.4
[13] iterators_1.0.6 limSolve_1.5.3 matrixStats_0.6.2
[16] parallel_2.15.2 preprocessCore_1.20.0 quadprog_1.5-4
[19] R.methodsS3_1.4.2 RColorBrewer_1.0-5 RCurl_1.95-3
[22] RSQLite_0.11.2 splines_2.15.2 stats4_2.15.2
[25] survival_2.37-2 tools_2.15.2 XML_3.95-0.1
[28] xtable_1.7-0
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