Chuanbao [guest] | 5 Feb 08:46 2013

GSVA error


I am a new-comer in R and am learning the Bio Package GSVA. I get the expression file and genesets from CSV
files by read.csv. And when I run GSVA by gsva(expr,genesets). there is an error message. That also
happened when I do as the instructions (where there are example data) tell
(http://www.bioconductor.org/packages/2.11/bioc/vignettes/GSVA/inst/doc/GSVA.pdf) .
Really appreciate your help~~~

 -- output of sessionInfo(): 

library(GSEABase)
library(GSVAdata)
library(Biobase)
library(genefilter)
library(limma)
library(RColorBrewer)
library(RBGL)
library(graph)
library(Rgraphviz)
library(GSVA)
data<-read.csv(file.choose(),head=T)
row.names(data)<-data$Symbol
data<-data[,-1]
expr<-data.matrix(data)
list<-read.csv(file.choose(),head=T)
row.names(list)<-list$Symbol
set1<-list[1:15,1]
set2<-list[16:30,1]
genesets<-list(set1,set2)
genegsva<-gsva(expr,genesets)

Testing 2 gene sets.
Computing observed enrichment scores
Computing gene densities
Error in .C("assess_matrix_density_R", as.double(t(expr[, sample.idxs])),  : 
  C symbol name "assess_matrix_density_R" not in load table

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