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Comment: lfcShrink and alpha value
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cropero
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Thank you for your fast answer, I have everything clear now
Answer: DESeq2 - Comparing Comparisons
by
James W. MacDonald
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Assuming that WC in your equation #2 is different in KD1 subunit1_vs_WC and SCR subunit1_vs_WC, this is just an interaction, and the easies…
Comment: Differential Expression Genes as Independent Variables
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James W. MacDonald
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An alternative to that is to use the `glmnet` package to fit a regularized regression using all proteins at once.
Comment: Differential Expression Genes as Independent Variables
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abadgerw
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Thanks. The proposal was not to include all proteins as covariates in one model but to iterate with one protein serving as the independent …
Answer: How to annotate a limma Elist raw class object with an annotation file
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James W. MacDonald
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Your first step when trying to use a function is to read the help page (`?mapIds`), which will bring this up:
```
Usage:
colu…
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