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Old 08-28-2018, 07:06 AM   #5
ckruse6
Junior Member
 
Location: Ohio, USA

Join Date: Aug 2018
Posts: 1
Cool Manual Calc option

So, I know it isn't ideal, but let's take the actual values of log(CPM) and log(FC) that you have from edgeR. Keep in mind this will only work if your replicates of experimental and control were equal, but you could tweak it as needed. Might be worth double checking that logCPM is using base 2 which I believe is default.

Using "A" to be the average expression of your experimental condition and "B" to be your control as you've run it.

FC=A/B, so
2^log(FC) will get you (A/B)
CPM=(A+B)/2, so
2^log(CPM)=(A+B)/2

Basic algebra solves for B,
B=2(2^log(CPM))/(1+2^(log(FC)))

and then
A= 2(2^log(CPM)) - B

Using the values of a typical EdgeR, this is minimal R work to generate the columns you wanted.

Hope this helps!
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