Bioconductor Blocking

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replies

678

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voom blocking limma

updated 6 months ago by Gordon Smyth 50k • written 6 months ago by Gerhard Thallinger ▴ 180

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690

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edgeR blocking

updated 2.9 years ago by Yunshun Chen ▴ 840 • written 2.9 years ago by Molly • 0

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916

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diffbind blocking model

updated 3.4 years ago by Rory Stark ★ 5.1k • written 4.5 years ago by melnuesch ▴ 10

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1.3k

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edger limma paired blocking ruvseq

updated 3.9 years ago by Gordon Smyth 50k • written 3.9 years ago by ScA • 0

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1.9k

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limma repeated measurements blocking random effects

updated 4.1 years ago by Gordon Smyth 50k • written 4.1 years ago by Jane ▴ 10

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3.6k

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limma edger blocking paired samples

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by anou ▴ 10

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803

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diffbind differential binding analysis blocking

updated 6.2 years ago by Rory Stark ★ 5.1k • written 6.3 years ago by zhangly811 • 0

7 results • Page 1 of 1

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Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10

Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…

Comment: Error in champ.load(): The following specified files do not exist by Sherin • 0

it worked! thank you so much!!

Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0

Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…

Comment: DESeq2 setting significant p-value by Michael Love 41k

It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.

Comment: Input Question for deseq.r by ATpoint ★ 4.0k

It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…

Votes

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

Comment: Reading huge bismark coverage files using bbseq::read.bismark

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