GSVA on enrichment scores about R project
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Entering edit mode
2.2 years ago
1466956114 • 0

Dear all,

I am trying to use GSVA for enrichment scores. I obtain data of gene expression matrix form TCGA, and the the genesets are created by myself as needed. I am a beginner in the R project and have done a lot of hard work, but I am still very confused. Input data format: Gene expression matrix:(for example) genename sample1 sample2 sample3 A 1 2 0 B 2 3 1 C 1 0 2 Genesets data: genesetname description gene geneset1 NA A B C geneset2 NA B D E

Can anyone please give me some suggestions how to use GSVA for my data analysis? Thanks very much. best XX

gene <- read.csv("C:\Users\86188\Desktop\expression.csv",header = TRUE,sep = ",") genesets <- getGmt("C:\Users\86188\Desktop\symbols.gmt") score <- gsva(gene, genesets,method= "ssgsea", + rnaseq=TRUE,abs.ranking=FALSE, min.sz=1, max.sz=Inf, no.bootstraps=0, bootstrap.percent = .632, parallel.sz=0, parallel.type="SOCK", mx.diff=TRUE, tau=switch(method, gsva=1, ssgsea=0.25, NA),kernel=TRUE,ssgsea.norm=TRUE,verbose=TRUE) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘gsva’ for signature ‘"data.frame", "GeneSetCollection"’

gsva RNA-Seq R • 1.2k views
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Entering edit mode
10 months ago
DBScan ▴ 20

The first error is because "gene" is a data.frame instead of a matrix (I had the same error same days ago too). The second error is because the GMT file has a wrong format I think. You can check the GMT format here: http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats

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