LRT test followed by filtering based on LFC
1
0
Entering edit mode
@sallybadawi-16174
Last seen 2.6 years ago

Good morning,

I know that LFC threshold and altHypothesis are applied only in Wald tests. Is there any way to sort out gene based on LFC thresholding post LRT test? LRT result tables usually provide pvalue of the tested hyposthesis and LFC for the specified conditions only. Would it be statistically relevant to do LRT test first, retrieve adj Pvalues and then do LFCthresholding on pairwise wald test and take obtained LFC for each condition separately?

Thank you fr your help,

Sally

deseq2 LFC LRT • 301 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 day ago
United States

You want just the LFC for each of the coefficients? See the vignette on “Access to all calculated values” or ?results on the LRT test.

ADD COMMENT
0
Entering edit mode

No, I know how to access all data, I want to sort after LRT test based on the LFC I want genes having absolute LFC > 0,5 but I cant use LFCthreshold in LRT test results. So how can I filter based on FC? Or you recommend that I dont do this filtering originally?

ADD REPLY
0
Entering edit mode

You can pull out the LFCs for individual coefficients that are dropped in the LRT, and then do simple filtering in R, right? Like you said, we don’t have any kind of combination lfcThresholding on multiple coefficients at once. Another way to go would be to use lfcThreshold and Wald tests and combine the pvalues.

ADD REPLY

Login before adding your answer.

Traffic: 168 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