Question

LRT test followed by filtering based on LFC

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sally.badawi • 0

@sallybadawi-16174

Last seen 5.8 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 • 1.8k views

ADD COMMENT • link written 5.8 years ago by sally.badawi • 0

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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

ADD REPLY • link 2.0 years ago Masker • 0

score 0 · Answer 1 · 2019-02-15

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Michael Love 42k

@mikelove

Last seen 48 minutes 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 • link 5.8 years ago Michael Love 42k

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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?

ADD REPLY • link 5.8 years ago sally.badawi • 0

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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.

ADD REPLY • link 5.8 years ago Michael Love 42k

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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?

ADD REPLY • link 2.7 years ago chm • 0

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

ADD REPLY • link 2.7 years ago Michael Love 42k