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Comment: Differential Expression Genes as Independent Variables
by
abadgerw
• 0
Thanks! I was thinking about this but do not believe glmnet allows for regularized mixed models unless I am mistaken?
Comment: lfcShrink and alpha value
by
cropero
• 0
Thank you for your fast answer, I have everything clear now
Answer: DESeq2 - Comparing Comparisons
by
James W. MacDonald
67k
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
by
James W. MacDonald
67k
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
by
abadgerw
• 0
Thanks. The proposal was not to include all proteins as covariates in one model but to iterate with one protein serving as the independent …
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A: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
C: How to bin a GRanges to small bins
A: deseq2 filter the low counts
A: deseq2 filter the low counts
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