Question: LRT test followed by filtering based on LFC
0
gravatar for sally.badawi
4 weeks ago by
sally.badawi0 wrote:

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 lrt lfc • 62 views
ADD COMMENTlink modified 4 weeks ago by Michael Love22k • written 4 weeks ago by sally.badawi0
Answer: LRT test followed by filtering based on LFC
0
gravatar for Michael Love
4 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

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 COMMENTlink written 4 weeks ago by Michael Love22k

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 REPLYlink written 4 weeks ago by sally.badawi0

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 REPLYlink modified 4 weeks ago • written 4 weeks ago by Michael Love22k
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