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

[Robert Castelo]

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
>
>
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>
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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