Entering edit mode
3.9 years ago
jacobelnaggar
▴
10
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)
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