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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> . >> > > -- > 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