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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