User: lefeverde

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lefeverde0
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Posts by lefeverde

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Comment: C: DESeq2 count outlier replacement from Cook's threshold
... Hi Michael! Thanks for getting back to me so quickly! I went back over your paper and the vignette and my interpretation was that the TMM replacement method would err on the side of false negatives rather than positives. This approach is conservative, it will not lead to false positives, as it repl ...
written 11 days ago by lefeverde0
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DESeq2 count outlier replacement from Cook's threshold
... I'm currently having some issues with how DESeq2 implements count outlier replacement when the number of samples suffices. From what I understand, the default is to use: 99% quantile of the F(p,m-p) My specific questions are: What is the rational behind the default Cook's distance threshold for ...
rnaseq deseq deseq2 outliers count outliers written 11 days ago by lefeverde0 • updated 11 days ago by Michael Love20k

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