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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
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ja569116
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Hi @atpoint Thanks for the information.
Could you please expand on when to use adjusted p-values vs nominal p-values.
My understanding was …
Answer: limpa analysis advice
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Gordon Smyth
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
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Gordon Smyth
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
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Gordon Smyth
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I updated the above answer today.
Answer: When to use edgeR or limma
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James W. MacDonald
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I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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