Question: CPM plot for individual genes
0
gravatar for iraia.munoa
5 months ago by
iraia.munoa70
iraia.munoa70 wrote:

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

tmm edger rna-seq cpm • 212 views
ADD COMMENTlink modified 5 months ago by ATpoint24k • written 5 months ago by iraia.munoa70
1

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

ADD REPLYlink written 5 months ago by ATpoint24k

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!

ADD REPLYlink modified 5 months ago by ATpoint24k • written 5 months ago by iraia.munoa70
1

The latter is what I would do.

ADD REPLYlink written 5 months ago by ATpoint24k

Well thanks!!! I will try!

ADD REPLYlink written 5 months ago by iraia.munoa70
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