Question

How to do DEGs based on CPM

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li.zhaoz ▴ 10

@lizhaoz-22033

Last seen 4.2 years ago

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 • 2.4k views

ADD COMMENT • link updated 5.0 years ago by Gordon Smyth 52k • written 5.0 years ago by li.zhaoz ▴ 10

score 5 · Answer 1 · 2019-12-03

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Gordon Smyth 52k

@gordon-smyth

Last seen 9 hours ago

WEHI, Melbourne, Australia

See limma User's Guide, Section 15.4.

ADD COMMENT • link 5.0 years ago Gordon Smyth 52k

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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 REPLY • link 5.0 years ago sergisayolspuig ▴ 80

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

ADD REPLY • link 5.0 years ago Gordon Smyth 52k