This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Deseq2 statistics treatment vs control

Hi!

In Deseq2 it has to be set which is control and which is treatment. Let's say I have 2 treatments - A and B and I run analysis so that A is control. If I now run the analysis again so that B is control and A treatment, would that change my result statistics or would just the up-regulated become down-regulated and vice versa?

Thanks!

rna-seq
• 3,448 views • link
written by JE • JE

3 answers

It should only change the sign of your log-FC differnetial expression calls

• 0 views • link
written by russhh russhh

I moved this to an answer, since it's the answer.

• 0 views • link
written by Devon Ryan Devon Ryan

Ok, thanks! So if I accidentally run the analysis with wrong control I could just multiply the lfc value by (-1) to get the values correct? The original analysis was run already some time ago and when I re-run it now with treatment as a control I get more DEGs with changed stats. Also the MA plot looks different (not just inverted positive and negative). So the reason for the difference is not changing the control but something else has been changed?

• 0 views • link
written by JE • JE

Is it possible that some other aspect of the alignment/quant/diffex workflow has changed in that time? Are you using the same versions of the tools etc

• 0 views • link
written by russhh russhh

The analysis was run in Oct 2016 so it is very likely that something has changed. The number of comparisons is bigger than 2 in my experiment and the control needs to be changed only for part of them. For all comparisons I should use exactly the same workflow and packages, right? So if I do not want to re-run the analysis for all data, I could just invert the lfc for the one I need? Just want to be absolutely sure I can do that :) Otherwise, if I re-run part of comparisons with changed packages I should repeat the analysis for all the rest of comparisons as well (that were done with correct control).

• 0 views • link
written by JE • JE

Removed content to comment :) thanks for instructions, my fist post here :)

• 0 views • link
written by JE • JE

Use the ADD COMMENT button for comments or furthers questions. Do not post questions as answers, please.

• 0 views • link
written by h.mon h.mon

Log in to answer this question.

More posts like this