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Question: GSA for comparison of geneset enricment analysis between multiple class
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gravatar for Seymoo
9 months ago by
Seymoo0
Oslo
Seymoo0 wrote:

I have a gene expression data `AllExp` and a data.frame `info` with sample name of `AllExp` as row names and first column in it specifies groups that each sample belongs to.

I am trying to perform a a gene set enrichment analysis using GSA package. but I get following error

`Error in cut.default(sd, br, labels = F) : invalid number of intervals`

GS <- Sys.glob("E:/gmts/h.all.v6.1.symbols.gmt")
GS <- GSA.read.gmt(GS)
GSA(AllExp, y=factor(info[,1]), genesets=GS$genesets, genenames = row.names(AllExp),method="maxmean", resp.type="Multiclass", minsize=10)

what is wrong with my code?

gsa
ADD COMMENTlink modified 9 months ago • written 9 months ago by Seymoo0
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