Hi!

I am working with my DEGs list from `edgeR`

with TMM normalization. I have seen in many publications that researches plot `log2(FPKM)`

values for individual DEGs to show the statistical significance. Regarding this, I would like to know if it is posible to plot the `log2(CPM)`

values of control and treatment samples for individual genes, as I have used `edgeR`

with TMM and not RPKM. Is there a function in `edgeR`

to obtain this values for control and treatment samples of each gene, instead of the total value of the final report? Or do I need to start with `featureCounts`

data and transform it somehow?
Can someone help me?

Thanks in advance!!

Iraia

You can get the TMM-corrected CPM values from your analysis, see output TMM normalized counts with edgeR. No need to start over.

Well I have been reading the link you showed me, but I am a little bite confused and don't understand what I need to run in

`edgeR`

. In the coments James Ashmore provides a cpm.DGEList function, do I need to run it like that? Or running`cpm(y, log=TRUE, lib.size=libsize, prior.count=2)`

after the`calcNormFactor()`

selecting TMM method is enough? Thanks again!The latter is what I would do.

Well thanks!!! I will try!