17 months ago • updated 7 months ago
shepherl
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19 months ago • updated 17 months ago
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written 5.7 years ago by
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2.1 years ago
shepherl
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2.6 years ago
pgauthi1
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2.6 years ago • updated 2.1 years ago
shepherl
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3.1 years ago • updated 2.6 years ago
shepherl
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4.0 years ago • updated 3.5 years ago
shepherl
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4.7 years ago
shepherl
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4.9 years ago
shepherl
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5.0 years ago
shepherl
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5.1 years ago • updated 5.0 years ago
shepherl
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5.2 years ago • updated 5.1 years ago
shepherl
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5.3 years ago • updated 5.2 years ago
shepherl
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5.5 years ago
shepherl
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5.5 years ago
shepherl
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Recent ...
Replies
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
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
▴
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
▴
350
Simply remove the cell type from the model.
design <- model.matrix(~targets$Status)
Answer: ANOVA like approach of edgeR
by
Yunshun Chen
▴
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
•
0
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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