Question: edgeR complex nested experiment
0
gravatar for joanna.l.kelley
4.3 years ago by
United States
joanna.l.kelley0 wrote:

Hi everyone, I'm looking at the example of a complex experimental design on the most recent (April 2015) on page 36
The example states "To find genes that respond to the hormone in any disease group:"
> lrt <- glmLRT(fit, coef=10:12)
> topTags(lrt)

I'm interested in identifying the genes that respond to hormone in all disease groups. How is the glm constructed to identify genes that respond in all disease groups?

Thank you!

edger • 491 views
ADD COMMENTlink modified 4.3 years ago by Aaron Lun24k • written 4.3 years ago by joanna.l.kelley0
Answer: edgeR complex nested experiment
1
gravatar for Aaron Lun
4.3 years ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

To do that, you'll have to test for an effect in each disease group, i.e., by dropping each coefficient individually. This will give you three sets of DE genes. You can intersect them to find the common set of genes that respond in all of the three disease groups (you might want to select by the sign of the log-fold change first, to ensure that you're picking genes that respond in the same manner in each group). I don't think it's possible to construct a GLM contrast for a composite null hypothesis.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Aaron Lun24k
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