Bioconductor Batch correction

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scrna-seq integration batch correction

updated 6.0 years ago by Aaron Lun ★ 29k • written 6.0 years ago by p.joshi ▴ 40

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1.8k

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methylation ComBat Linear models batch correction AIC

updated 6.1 years ago by Kevin Blighe ★ 4.0k • written 6.2 years ago by lucasmiranda42 • 0

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1.1k

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DESeq2 batch correction

updated 6.2 years ago by James W. MacDonald 68k • written 6.2 years ago by MT ▴ 10

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1.5k

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Diffbind ATAC batch correction blocking factor

updated 6.5 years ago by Rory Stark ★ 5.2k • written 6.5 years ago by rm1238 • 0

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deseq2 differential expression batch correction design

updated 6.6 years ago by Michael Love 43k • written 6.6 years ago by wunderl ▴ 40

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2.1k

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deseq2 differential expression batch correction

updated 6.6 years ago by Michael Love 43k • written 6.6 years ago by wunderl ▴ 40

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2.7k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 6.8 years ago by Vladimir Kiselev ▴ 150 • written 6.8 years ago by hamza_karakurt ▴ 60

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Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0

Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…

Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k

The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …

Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0

Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …

Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0

Thank you!

Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0

Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …

Votes

A: DESeq2 - VST eliminates zero values

Comment: Normalise to a housekeeping gene in DESEq2

Comment: limpa analysis advice

C: AnnotationForge makeOrgPackage rsqlite_send_query error

Answer: Limpa Pipeline Order

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