Bioconductor Batch Correction

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1.8k

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scrna-seq integration batch correction

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.9 years ago by p.joshi ▴ 40

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1.2k

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methylation ComBat Linear models batch correction AIC

updated 5.0 years ago by Kevin Blighe ★ 4.0k • written 5.0 years ago by lucasmiranda42 • 0

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762

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DESeq2 batch correction

updated 5.0 years ago by James W. MacDonald 67k • written 5.0 years ago by MT ▴ 10

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1.1k

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Diffbind ATAC batch correction blocking factor

updated 5.3 years ago by Rory Stark ★ 5.2k • written 5.3 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.4 years ago by Michael Love 42k • written 5.4 years ago by wunderl ▴ 40

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1.6k

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deseq2 differential expression batch correction

updated 5.4 years ago by Michael Love 42k • written 5.4 years ago by wunderl ▴ 40

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.6 years ago by Vladimir Kiselev ▴ 150 • written 5.6 years ago by hamza_karakurt ▴ 60

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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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