Bioconductor Ashr

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DESeq2 apeglm DESeq ApeGLM Ashr

updated 16 months ago by Michael Love 42k • written 16 months ago by Ndimensional ▴ 20

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Ashr LFCShrinkage IHW DESeq2

2.9 years ago Bex • 0

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ashr DESeq2 apeglm

updated 3.2 years ago by Michael Love 42k • written 3.3 years ago by Guandong Shang ▴ 40

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ashr DESeq2 lfcShrink svalue

3.7 years ago Enrico • 0

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deseq2 ashr

4.1 years ago da.de ▴ 30

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deseq2 ashr rna-seq

4.6 years ago Alex • 0

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766

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ashr

4.6 years ago kavator ▴ 30

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ashr Deseq2 lfcThreshold

updated 3.1 years ago by Michael Love 42k • written 4.6 years ago by Iryna • 0

8 results • Page 1 of 1

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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 ▴ 880

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 ▴ 880

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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Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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