Question: How to do DEGs based on CPM
0
gravatar for li.zhaoz
11 days ago by
li.zhaoz0
li.zhaoz0 wrote:

I only have CPM value available. Just wondering if I could take the logCPM and put it input limma with trend = TRUE. That is what the voom paper descirbed if I get it right. Any advice? Thank you!

limma • 86 views
ADD COMMENTlink modified 10 days ago by Gordon Smyth39k • written 11 days ago by li.zhaoz0
Answer: How to do DEGs based on CPM
2
gravatar for Gordon Smyth
10 days ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

See limma User's Guide, Section 15.4.

ADD COMMENTlink written 10 days ago by Gordon Smyth39k
1

Dear Gordon,

shouldn't the last chunk of code in Section 15.4 be (notice the trend=TRUE parm)?

Or, to give more weight to fold-changes in the gene ranking, one might use:

> fit <- lmFit(logCPM, design)
> fit <- treat(fit, lfc=log2(1.2), trend=TRUE)
> topTreat(fit, coef=ncol(design))

ADD REPLYlink modified 10 days ago • written 10 days ago by sergisayolspuig50

Yes, that is true. I will add the trend = TRUE.

ADD REPLYlink written 9 days ago by Gordon Smyth39k
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