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From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
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> the results are not satisfactory to me
Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
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It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
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For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
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