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)