Optimal edgeR design for a single-factor experiment
1
0
Entering edit mode
Alex • 0
@00c53394
Last seen 3.5 years ago
United States

Hi all,

I'm a budding researcher learning edgeR primarily by reading through the official User's Guide. I'm analyzing an RNA-seq dataset with six samples, three in each of two groups. I found the User's Guide a bit cryptic as to whether I should use the classic edgeR approach (exactTest) or the GLM functionality (glmQLFTest). I understand the classic approach is useful for experiments with only a single factor, like mine, but the authors of the User's Guide often used the glm approach in examples even with a single factor. Any tips?

```

factors edgeR setup DGELIst • 1.1k views
ADD COMMENT
1
Entering edit mode
@gordon-smyth
Last seen 4 hours ago
WEHI, Melbourne, Australia

We currently recommend glmQLFTest for all bulk RNA-seq experiments with replicates because it gives better error rate control than other approaches. It is just as easy to apply as the classic exactTest approach but provides lots more options. See for example

ADD COMMENT

Login before adding your answer.

Traffic: 608 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6