Question: EdgeR for RNA-Seq
gravatar for aj123
4.6 years ago by
United States
aj12370 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")


rna-seq bioconductor R • 1.7k views
ADD COMMENTlink modified 4.6 years ago by Alex Reynolds30k • written 4.6 years ago by aj12370
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 972 users visited in the last hour