[BioC] GSVA error
Robert Castelo
robert.castelo at upf.edu
Tue Feb 5 09:02:58 CET 2013
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
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