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Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
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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 …
Answer: How to annotate a limma Elist raw class object with an annotation file by James W. MacDonald 67k
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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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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