Troubleshooting DESeq2 Analysis: no DE genes found in subset
Entering edit mode
Last seen 10 days ago
United States


I'm quite new to R and DESeq2 and need some help troubleshooting! I'm working on analyzing a dataset comparing 3 groups: patients before and after a treatment against a healthy control (not given treatment).

For the first analysis I wanted compare MDD patients before and after, so I originally subset the data-frame to include just the MDD patients, and then created a factor to describe the timepoint, filtered the counts, and performed a DESeq2 analysis. With this, we get 0 DE genes. In other analysis, such as health control versus patients before treatment, we get anywhere between 0-6 DE genes.... so, something isn't quite working with this method.

It was suggested that we feed DESeq2 all of our data in order to improve the statistical power and then select an analysis within the function using the interaction argument, but after reading the Bioconductor manual this doesn't seem very applicable since our control group doesn't have a before and after, just one timepoint.

Does anyone have any suggestions as to how to better perform this analysis?

Thank you!

DESeq2 • 249 views
Entering edit mode

Doesn't sound to me like interactions are appropriate. You have before, after, control. Three levels of one factor.

Entering edit mode
Last seen 1 day ago
United States

so, something isn't quite working with this method.

I don't see how you conclude something isn't working. It sounds like either you have no DE or you have insufficient power to detect what is there.


Login before adding your answer.

Traffic: 290 users visited in the last hour
Help About
Access RSS

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

Powered by the version 2.3.6