LRT test followed by filtering based on LFC
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Last seen 4.1 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?

Sally

deseq2 LFC LRT • 842 views
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I have full access to the information, and now I need to sort it based on the LRT result and the LFC. To get the desired results from the LRT test, you cannot use the LFCthreshold criterion. My question is, how do I use FC to narrow my search resultst for bubble shooter

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@mikelove
Last seen 14 hours 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.

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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?

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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.

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"You can pull out the LFCs for individual coefficients that are dropped in the LRT" , is it present in the manual how to do it?

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See ?results Details section "For analyses using the likelihood ratio test..."