Biostar Voomwithqualityweights

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2.1k

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limma voomwithqualityweights gene set analysis

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.8 years ago by BharathAnanth ▴ 70

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1.1k

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limma RNA-Seq voom voomWithQualityWeights edgeR

updated 2.9 years ago by Gordon Smyth 47k • written 2.9 years ago by pedrodcb • 0

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842

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limma edger voom voomWithQualityWeights limma-voom

updated 5.2 years ago by Gordon Smyth 47k • written 5.2 years ago by Guido Hooiveld ★ 3.5k

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1.0k

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limma t-statistic voom voomwithqualityweights robust regression

4.2 years ago brynedal ▴ 30

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1.5k

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voomwithqualityweights limma voom duplicatecorrelation

updated 4.6 years ago by Aaron Lun ★ 28k • written 4.6 years ago by BharathAnanth ▴ 70

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3.2k

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voomWithQualityWeights output

updated 5.2 years ago by Gordon Smyth 47k • written 5.2 years ago by harelarik ▴ 60

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713

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limma lmfit voom limma design matrix voomwithqualityweights

updated 4.1 years ago by Gordon Smyth 47k • written 4.1 years ago by kediggins ▴ 10

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608

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limma voom RNA-seq voomWithQualityWeights

updated 3.7 years ago by Matthew Ritchie ▴ 1000 • written 3.7 years ago by Julien Roux ▴ 90

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2.9k

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voom limma-voom voomwithqualityweights rna-seq

updated 5.0 years ago by Matthew Ritchie ▴ 1000 • written 5.0 years ago by anne.biton ▴ 20

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Answer: collapseReplicates error after tximeta by Michael Love 39k

The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…

Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k

That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…

Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k

You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…

Answer: Which genes are outliers in DESeq2? by Michael Love 39k

Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…

Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by Michael Love 39k

Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…

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Significant reporter activity with mpralm function

Answer: I cannot install annotables package in Rstudio (macOS)

Answer: log2 of normalized counts for further analyzes

Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it

Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used

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