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iDEP-SDSU / idep

Integrated Differential Expression and Pathway analysis
http://ge-lab.org/idep
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Using full EdgeR DEG analysis #215

Open remybonnav opened 1 year ago

remybonnav commented 1 year ago

Hi, thanks a lot for this great software.

Are you planning to add EdgeR TMM normalization and using this for DEG?

I don't understand what the CPM function of EdgeR is doing compared to a simple function obtained by dividing counts by the library counts sum and multiplying the results by a million? Iin iDEP, does the CPM function of EdgeR is actually giving the CPM after normalizing the library using TMM?

Thanks a lot in advance.