[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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