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Can I Calculate LogCPM with raw counts?

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?

edger biomart maplot de logcpm
• 8,577 views • link
updated by Ram Ram • written by rodolpho.gheleri • rodolpho.gheleri

you mean something like this?

>library(edgeR)
>cpm(readcounts, log=TRUE)
• 0 views • link
written by Israel Barrantes Israel Barrantes

1 answer

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

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written by Irsan Irsan

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