updated 7.1 years ago by
mattia pelizzola
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written 7.1 years ago by
ma1478
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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
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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…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
by
rcreed
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0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di
by
James W. MacDonald
67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
Oh, i didn't realize there is another method in the mix here.
I would not necessarily trust this "batch correction" method, and suspect o…
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