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Answer: What type of counts data to import for performing Isoform analysis in edgeR
by
ATpoint
★
4.5k
You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…
Comment: Merge Replicates vs Mixed Model
by
abadgerw
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0
Thanks, @gabrielhoffman
The data is actually proteomics so it is intensity data which is why I did not use voom but rather ran ebayes wi…
Comment: ANOVA like approach of edgeR
by
Gordon Smyth
52k
To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …
Comment: DESeq2 sizefactors counfounded with biological treatment
by
Anna
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0
Hi James,
Apologies (re: posting in the wrong place).
Thank you so much for your response, that was exactly the help I needed.
Best,
A…
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