EdgeR for RNA-Seq

Question

[aj123]

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!