[BioC] GSVA error

[Robert Castelo]

Dear Chuanbao,

at the first sight it looks like some problem with the installation 
and/or loading of the library, since it contains some compiled C code 
that is not being found when the R code is invoking it. I would need 
more details to try to diagnose your problem more precisely.

could you please:

1. a formal aspect. i see that you've used the "Bioconductor Guest 
Posting" form, if you use this way to post questions at the BioC list, 
in future posts please paste your question and code in the text box code 
called "Question:"

2. please paste the output of the R command sessionInfo() in the text 
box entitled "Paste the output of the R command sessionInfo() below:"

3. show me the results of the commands:

dim(expr) ## lookup the dimension of the expression data matrix

expr[1:5, 1:5] ## inspect the first few cells of this matrix

genesets ## inspect the contents of the two gene sets


thanks,
robert.

On 02/05/2013 08:46 AM, Chuanbao [guest] wrote:
>
> 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
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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