Question: edgeR - DE with one disease sample vs. multiple control samples?
1
gravatar for RafaelMP
4 months ago by
RafaelMP110
Brazil
RafaelMP110 wrote:

Hello! I am trying to use RNA-seq data to accomplish two objectives in a case vs. control study:

1 - Verify if the expression level is distinct between the case sample and the controls.

2 - We need to identify DE genes between conditions.

Unfortunately, we have only one case with the mutation, but we have six biological replicates for the control group. Is it ok to use the package edgeR, or we need to try something else?

Thanks!

sequencing rna-seq next-gen R • 261 views
ADD COMMENTlink modified 4 months ago by Gordon Smyth840 • written 4 months ago by RafaelMP110
7
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth840
Australia
Gordon Smyth840 wrote:

There's no problem with this. edgeR handles unequal sample sizes automatically. It will simply estimate variability (i.e., the dispersion parameter) from the controls, where you do have replicates, and will then apply the same dispersion values to both cases and controls when conducting tests and computing fold changes.

This is a frequently asked question:

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth840
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