Bioconductor Batch correction

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2.2k

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scrna-seq integration batch correction

updated 5.8 years ago by Aaron Lun ★ 29k • written 5.8 years ago by p.joshi ▴ 40

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1.6k

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methylation ComBat Linear models batch correction AIC

updated 5.9 years ago by Kevin Blighe ★ 4.0k • written 5.9 years ago by lucasmiranda42 • 0

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962

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DESeq2 batch correction

updated 6.0 years ago by James W. MacDonald 68k • written 6.0 years ago by MT ▴ 10

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1.4k

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Diffbind ATAC batch correction blocking factor

updated 6.2 years ago by Rory Stark ★ 5.2k • written 6.2 years ago by rm1238 • 0

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1.4k

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deseq2 differential expression batch correction design

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by wunderl ▴ 40

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2.0k

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deseq2 differential expression batch correction

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by wunderl ▴ 40

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2.5k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.6 years ago by Vladimir Kiselev ▴ 150 • written 6.6 years ago by hamza_karakurt ▴ 60

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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

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Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

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