Diff Gene Expression On Multiple Biological Conditions : Deseq

Question

[Abhi]

Hey Guys

I am wondering if I can use DESeq for comparing genes expression across multiple biological conditions (I have 4 of them ) and not just 2. Based on what I have read from the vignette it seems like the package expects two condtions (eg treated v/s control) I guess one way to do it is to do pairwise comparison but just wondering if I can take your opinion.

Thanks! -Abhi

Answer 1

[Gireesh K. Bogu]

You can use DEB web-interface to run DESeq along with several other RNA-Seq software. You can access this at http://www.ijbcb.org/DEB/php/onlinetool.php This works well, if you have multiple conditions but not single. It accepts read-counts format. You can get this by using BED tools.

Good luck

[me.sr1510]

Is there any offline tool for the same? I have a similar situation.