Running Roast with Gene Symbols of Curated Genes
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lattalic • 0
@lattalic-10831
Last seen 5.3 years ago

I am running gene set analysis on curated gene sets from the MSigDB. I was successfully able to run roast using the following coding

library("edgeR")
summarized.counts <- read.table("C:/Users/Alicia/Documents/summarized.counts.matrix", row.names=1, header=TRUE, sep="\t")
design_two<-model.matrix(~0+ factor(c(1,1,1,2,2,2,3,3,3)))
colnames(design_two)<-c("stage1", "stage2", "stage3")
con<-makeContrasts(stage3-stage1, levels=design_two)
library(org.Hs.eg.db)
gene_set<-c("CYSLTR2", "GPR17","LTB4R", "LTB4R2", "GNB5", "GIP", "GNB2", "SCT", "VIP", "GNG8")
ind<-ids2indices(gene_set, row.names(summarized.counts))
ind
dge.edgeR=DGEList(counts=summarized.counts)
dge.edgeR<-calcNormFactors(dge.edgeR)
dge.edgeR=estimateDisp(dge.edgeR, design_two, robust=TRUE)
rst<-mroast(dge.edgeR, index=ind, design=design_two, nrot=9999, contrast=con)
rst

I am concerned about my results though. 

   NGenes  PropDown    PropUp Direction PValue    FDR PValue.Mixed FDR.Mixed
Set1      3 0.3333333 0.6666667        Up 0.0626 0.0626        1e-04     1e-04

Why would the output indicate a NGene number of 3 when I included 10 genes in my set?

(this is just practice data, my final gene sets will contain larger quantities of gene"

mroast roast gene set gene set analysis edgeR • 682 views
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@james-w-macdonald-5106
Last seen 9 hours ago
United States

The ids2indices function just looks at the (in your case) row.names of your gene counts, and finds which of them are in your gene_set. In this case there were only three genes in your gene_set that were also in the row.names of your gene counts. You could test that yourself by doing

sum(row.names(summarized.counts) %in% gene_set)
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Thanks, I figured that was the issue was I'm not super confident with this stuff yet. I really appreciate your help and that command line you provided. 

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