Bioconductor Batch Correction

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1.9k

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scrna-seq integration batch correction

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by p.joshi ▴ 40

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1.3k

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methylation ComBat Linear models batch correction AIC

updated 5.1 years ago by Kevin Blighe ★ 4.0k • written 5.1 years ago by lucasmiranda42 • 0

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783

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DESeq2 batch correction

updated 5.2 years ago by James W. MacDonald 67k • written 5.2 years ago by MT ▴ 10

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1.2k

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Diffbind ATAC batch correction blocking factor

updated 5.4 years ago by Rory Stark ★ 5.2k • written 5.4 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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1.7k

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deseq2 differential expression batch correction

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by wunderl ▴ 40

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.8 years ago by Vladimir Kiselev ▴ 150 • written 5.8 years ago by hamza_karakurt ▴ 60

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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by James W. MacDonald 67k

How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…

Comment: MBDseq analysis using qsea package by kf • 0

Hi Matthias, Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…

Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Quang • 0

Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…

Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D by ATpoint ★ 4.6k

It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…

Comment: Deseq2, enrichGO and ensembl ID by James W. MacDonald 67k

I am not sure I understand. You say that a unique Ensembl ID maps to multiple gene symbols. That doesn't mean you have two genes (it's just…

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A: Trajectory analysis for single cell sequencing

Answer: Annotation with org.Hs.eg.db Genome Build 38

Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool

A: goana limma- extract list of DE genes and genes in the enriched GO terms?

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