Perform DESeq2 with all conditions or separately, when condition is artificially created ?
0
0
Entering edit mode
2.6 years ago
Minh-Anh ▴ 10

Hello,

I have been wondering whether or not to include my vital status condition (Alive or Dead) along my inflammatory groups, which are artificially created prior to DESeq2 analysis. I am aware of https://support.bioconductor.org/p/101447/ and the FAQ where it is recommended to run DESeq2 along with all samples and all conditions, except when the data among a group has high variance.

However since my inflammatory group condition is artificially created out of the data set (by doing a mean of Z-score of an inflammation signature, and ranking the samples into multiple groups), I am not sure if combining every condition is a then a good idea.

What is confusing is that DESeq2 with vital status alone as design or with both vital status and inflammatory group as design, while extracting vital status as contrast, doesn't give the same result. and I don't know which one should be more appropriate and correct.

DESeq2 condition • 376 views
ADD COMMENT

Login before adding your answer.

Traffic: 2371 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6