Bioconductor Batch Correction

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1.8k

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scrna-seq integration batch correction

updated 4.9 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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769

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DESeq2 batch correction

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 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 5.5 years ago by Michael Love 43k • written 5.5 years ago by wunderl ▴ 40

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1.6k

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deseq2 differential expression batch correction

updated 5.5 years ago by Michael Love 43k • written 5.5 years ago by wunderl ▴ 40

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.7 years ago by Vladimir Kiselev ▴ 150 • written 5.7 years ago by hamza_karakurt ▴ 60

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Comment: Running multiple KNN queries in parallel by SamGG ▴ 360

Thank you for your detailed answer, I appreciate it and your work.

Answer: Running multiple KNN queries in parallel by Aaron Lun ★ 28k

That is correct - you can't pass the prebuilt objects to different processes. Maybe `MulticoreParam()` might work on POSIX systems but I'm …

Answer: RSubread output significantly different from bash Subread output by Gordon Smyth 52k

The difference (as ATpoint has correctly pointed out) is that Rsubread::featureCounts counts multi-mapping reads by default whereas the com…

Answer: Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square by Michael Love 43k

I would check the rank of your model matrix, and perhaps meet with a local statistician who can help you create an appropriate design matri…

Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170

Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.

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Answer: Running multiple KNN queries in parallel

Answer: RSubread output significantly different from bash Subread output

Answer: How to annotate a limma Elist raw class object with an annotation file

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Scholar to Aaron Lun ★ 28k

Teacher to Michael Love 43k

Popular Question to Dario Strbenac ★ 1.5k

Scholar to ATpoint ★ 4.6k