Question: EdgeR for RNA-Seq
0
gravatar for aj123
3.9 years ago by
aj12380
United States
aj12380 wrote:

Hi all,

I am new to this-this is actually the sequence of commands I am using in edgeR. Please let me know if it is correct or not. I believe first I have to "read the table" into R?

cpms = cpm(countdata)
keep = rowmeans(cpms >1) >= 2
countdata = countdata[keep,]
group <- factor(c(1,1,2,2))
dge = DGEList(counts=countdata,group=group)
dge <- calcNormFactors(dge)
dge <- estimateCommonDisp(dge)
dge <- estimateTagwiseDisp(dge)
et <- exactTest(dge)
etp <- topTags(et, n=30)
etp$table$logFC = -etp$table$logFC
head(etp, n=15)
write.csv(etp$table, "edgeR-control-vs-treatment.csv")

thanks!

rna-seq bioconductor R • 1.5k views
ADD COMMENTlink modified 3.9 years ago by Alex Reynolds28k • written 3.9 years ago by aj12380
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