Perform DESeq2 based on paired sample test

usegalaxy.org support
1

I want to use DESeq2 to compare between samples before treatment and after treatment individually as paired samples.
For example
Pt.1 before vs Pt.1 after
Pt.2 before vs Pt.2 after
Pt.3 before vs Pt.3 after
…
I followed this tutorial:

But I’m not sure if the DESeq2 in the above tutorial it compares patients individually or as a group, and How to do DESeq2 for paired samples for each patients individually in usegalaxy?

2

Dear @wmsalsah,
DESeq2 would group them.

You would need to apply DeSeq2 to each pair individually. I am not sure, if there is a more handy approach to this.

Kind regards,
Florian

1 Like
3

Thank you Florian