Running GSVA using open source RNA seq data
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5 months ago

Can someone kindly help me get practice using the package bioconductor GSVA using RNA seq data. I would just like to create a simple heatmap comparing the genesets/patways in two cancer types. The data I wanted to work with is found here.

I have been trying to follow tutorials online, however I am getting stuck trying to convert the data into a usable expression set and running the GSVA command to get the enrichment scores to then use to create a heatmap.

Any assistance would be greatly appreciated. Thank you!

edit: section of code I have been working on

library(limma)
library(GSVA)
library(GSVAdata)
library(org.Hs.eg.db)
library(GSEABase)
library(snow)
library(rlecuyer)
library(edgeR)

data(c2BroadSets)
gene.sets <- GeneSetCollection(c2BroadSets)

data <- read.table("HiSeqV2",header=TRUE,row.names=1,sep="\t")
data_exp <- <-new("ExpressionSet", exprs=as.matrix(data))

#having issues making this a valid expression list
filtered_eset <- nsFilter(data_exp, require.entrez=TRUE, remove.dupEntrez=TRUE,
                          var.func=IQR, var.filter=TRUE, var.cutoff=0.5, filterByQuantile=TRUE,
                          feature.exclude="^AFFX")

#having issues getting the GSVA function to run
topMatrixGSVA <- gsva(data_exp, gene., min.sz=10, max.sz=999999, abs.ranking=FALSE, verbose=TRUE)
RNA-Seq R gene GSVA Tutorial • 418 views
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Could you post the errors or messages you get ? "Having issues making/getting" doesn't help much to identify the possible source of confusion/error

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