Can I Calculate LogCPM with raw counts?

Question

[rodolpho.gheleri]

Hi everybody!

I am a novice bioinformatic yet, so here goes what I'm trying to do.

I receive a DE analysis from Biomart from other person and I want know if is possible to calculate LogCPM (average intensity) to plot a MAplot or Smear like edgeR by myself. I think I could get the raw counts to do that.

Can someone give a light, please?

[Israel Barrantes]

you mean something like this?

>library(edgeR)
>cpm(readcounts, log=TRUE)

[rodolpho.gheleri]

Thanks, I Could solve it!

Answer 1

[Irsan]

If you have the raw counts you can do that. Just carefully read the edgeR manual which walks you through the steps.

[rodolpho.gheleri]

Thanks, I Could solve it!