[BioC] Error when running Gene Set Variant Analysis (GSVA)

[Lucas Santana dos Santos]

Thank you all for your feedback.
I have updated the R and bioconductor versions and it seems to be working now...

Best,

Lucas 

On Jun 11, 2013, at 5:31 AM, Robert Castelo <robert.castelo at upf.edu> wrote:

> Dear Lucas,
> 
> you're missing the call
> 
> data(c2BroadSets)
> 
> which will load the 'c2BroadSets' object you are trying to access.
> 
> also, let me recommend you to upgrade to the latest version by upgrading first to R-3.0.x. in case of doubt, please consult:
> 
> http://www.bioconductor.org/install
> 
> cheers,
> robert.
> 
> On 06/10/2013 10:34 PM, Lucas Santana dos Santos wrote:
>> Hi All,
>> 
>> I have been trying to run GSVA analysis, but I keep getting the same error:
>> 
>> Error in get(as.character(FUN), mode = "function", envir = envir) :
>>   object 'FUN' of mode 'function' was not found
>> 
>> This keeps appearing no matter what data I use.
>> Here is my GSVA test code using the data from the GSVAdata package (as described in the GSVA user's manual):
>> 
>> library(GSVAdata)
>> library(GSVA)
>> data(commonPickrellHuang)
>> canonicalC2BroadSets<- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),grep("^REACTOME", names(c2BroadSets)),grep("^BIOCARTA", names(c2BroadSets)))]
>> esrnaseq<- gsva(pickrellCountsArgonneCQNcommon_eset, canonicalC2BroadSets, min.sz=5, max.sz=500, mx.diff=TRUE, verbose=FALSE, rnaseq=TRUE, parallel.sz=1)
>> 
>> My sessionInfo():
>> 
>> R version 2.15.3 (2013-03-01)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>>  [1] GSVA_1.6.6           foreach_1.4.0        biomaRt_2.14.0       DESeq_1.10.1         lattice_0.20-13
>>  [6] locfit_1.5-9         edgeR_3.0.8          limma_3.14.4         GSEABase_1.20.2      graph_1.36.2
>> [11] annotate_1.36.0      AnnotationDbi_1.20.7 Biobase_2.18.0       BiocGenerics_0.4.0   mvbutils_2.7.4
>> 
>> loaded via a namespace (and not attached):
>>  [1] codetools_0.2-8    DBI_0.2-5          doParallel_1.0.1   genefilter_1.40.0  geneplotter_1.36.0 grid_2.15.3
>>  [7] IRanges_1.16.6     iterators_1.0.6    parallel_2.15.3    RColorBrewer_1.0-5 RCurl_1.95-4.1     RSQLite_0.11.2
>> [13] splines_2.15.3     stats4_2.15.3      survival_2.37-2    XML_3.96-1.1       xtable_1.7-1
>> 
>> Any ideas about what is the cause of error?
>> 
>> Many thanks,
>> 
>> Lucas
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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>> 
> 
> -- 
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550