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Comment: DESeq2: Variable Importance
by
lolol
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0
Ah yes, I see the deviance now in mcols. Would I use this to calculate the pseudo R-squared (McFaddens), comparing each model with a single…
Answer: How to do annotation with Limma
by
Guido Hooiveld
★
3.0k
For the HTA2.0 arrays should not use `hgu95av2.db`, which is the annotation library for the, ehh, human U95 set of Affymetrix arrays! You s…
Comment: DESeq2: Variable Importance
by
Michael Love
33k
Yes, `deviance` is an output in the `mcols`, so you could rotate through variables, excluding them in the LRT. Or you could use the other p…
Answer: Hard coding in DiffBind DBA.R line 968
by
Rory Stark
★
3.9k
Thank you for noticing and reporting this potential issue relating to the minimum number of sample replicates required to form a contrast.
…
Comment: DESeq2: Variable Importance
by
lolol
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When you say observing the deviance, you mean utilizing the likelihood ratio test with the reduced model (exclude the last variable). Am I …
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