updated 22 months ago by
Christian Mertes
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written 2.0 years ago by
me.achleitner
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updated 2.9 years ago by
Gordon Smyth
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written 3.4 years ago by
Brian
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3.3 years ago • updated 2.0 years ago
soda
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Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
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I'm adding my comment to the threaded section ...
I don't have any suggestions here but whatever method you're using is not appropriate up…
Comment: ANOVA like approach of edgeR
by
Yunshun Chen
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870
If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …
Comment: ANOVA like approach of edgeR
by
SamGG
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Simply remove the cell type from the model.
design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR
by
Yunshun Chen
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870
You could try the followings:
> design <- model.matrix(~ 0 + group)
> contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…
Answer: Identical samples after deseq2 batch effect removal
by
maripane
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Thanks Michael, so is there a way to work around this issue?
Can I somehow make sure I can remove this batch effects without overcorrecti…
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