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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…
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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…
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Thank you for noticing and reporting this potential issue relating to the minimum number of sample replicates required to form a contrast.
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AT
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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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> In general, what are the best practices for environment reproducibility with biocondcutor packages?
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