Bioconductor Batch correction

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1.0k

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scrna-seq integration batch correction

updated 3.4 years ago by Aaron Lun ★ 28k • written 3.4 years ago by p.joshi ▴ 40

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618

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methylation ComBat Linear models batch correction AIC

updated 3.5 years ago by Kevin Blighe 3.8k • written 3.5 years ago by lucasmiranda42 • 0

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402

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DESeq2 batch correction

updated 3.6 years ago by James W. MacDonald 63k • written 3.6 years ago by MT ▴ 10

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608

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Diffbind ATAC batch correction blocking factor

updated 3.8 years ago by Rory Stark ★ 4.9k • written 3.8 years ago by rm1238 • 0

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692

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deseq2 differential expression batch correction design

updated 4.0 years ago by Michael Love 40k • written 4.0 years ago by wunderl ▴ 40

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919

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deseq2 differential expression batch correction

updated 4.0 years ago by Michael Love 40k • written 4.0 years ago by wunderl ▴ 40

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1.3k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 4.2 years ago by Vladimir Kiselev ▴ 150 • written 4.2 years ago by hamza_karakurt ▴ 50

7 results • Page 1 of 1

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Comment: Interpret plot from DiffBind by Chris • 0

I sorted Fold decreasing. When I filter out genes with fold > 2.5 and filter out genes with fold < -2.5 and got 1287 genes appear in both s…

Comment: Interpret plot from DiffBind by Chris • 0

Thank you so much. I think the function is `dba.report()`. more_open_in_disease: 79113 more_closed_in_disease: 36828 So there are 79113 pea…

Comment: Interpret plot from DiffBind by Chris • 0

Hi Rory, when I run your code, I got this error: Error: unexpected ')' in: " matrices_color=list(c("white", "ma…

Comment: Can DESeq2 handle huge variations in sequencing depth among samples? by Gopinath • 0

Thanks for your suggestion, Michael. I will try that strategy.

Comment: Error with IsoformSwitchAnalyzer: analyzePFAM by Callum • 0

It seems that the problem doesn't occur when the input file is significantly shortened to ~20 transcripts! Please help

Votes

A: ggbio error: Objects of type OrganismDb not supported by autoplot

Answer: DeSEQ 2 Error: some values in assay are negative

DESeq2 Error from Installing a Package

Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)

Comment: Error: biomaRt has encountered an unexpected server error.

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