User: lefeverde

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lefeverde10
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Posts by lefeverde

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Comment: C: DESeq2 Dose not work
... I feel like I've had a similar problem with another package before. It had something to do with only source version of the package being available. Try installing the packages that give you an error manually. For example, where it says: `there is no package called ‘rlang’ dds` Manually install `rlan ...
written 11 weeks ago by lefeverde10
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Comment: C: prepDE KeyError on MSTRG
... KeyError means you're trying to use a key which doesn't exist. I think that might mean you have different transcripts in your sample gtf files.  ...
written 4 months ago by lefeverde10
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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 4 months ago by lefeverde10
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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 4 months ago by lefeverde10 • updated 4 months ago by Michael Love23k

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