User: zefrieira

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Posts by zefrieira

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Using altHypothesis with shrunken LFC values in DESeq2
... Currently, the only way to use `altHypothesis` in DESeq2 is through `results`. However, this doesn't allow to use `altHypothesis` in shrunken LFC values. I want to isolate genes with low LFC and I'm using `altHypothesis="lessAbs"` for that, but, as my LFC values were not shrunken, I think I may be u ...
deseq2 written 3 months ago by zefrieira0 • updated 3 months ago by Michael Love25k
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Answer: A: deseq2 pre filter rna seq
... DESeq2 filters genes based on their counts. Read the [independent filtering section][1] of the documentation. [1]: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#indfilttheory ...
written 3 months ago by zefrieira0
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Comment: C: Using alternative LFC shrinkage methods for computing p-values in DESeq2
... Thank you very much! Is there a reason you recommend [using a stricter threshold for s-values][1]? Is this something you observed empirically? Also, are there any plans to unify the interface for getting significance levels based on shrunken LFC? Right now, there are two different interfaces: - ...
written 4 months ago by zefrieira0
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Using alternative LFC shrinkage methods for computing p-values in DESeq2
... In [this post][1], Mike Love explained the reasoning for moving LFC shrinkage into its own step using the `lfcShrink` function, decoupling testing from shrinkage. Is there any way to use `apeglm`-shrinked LFC to compute p-values (similar to using `betaPrior=TRUE`, but with the new estimator)? I kn ...
deseq2 statistics apeglm written 4 months ago by zefrieira0 • updated 4 months ago by Michael Love25k

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