Biostar Hypergeometric

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overrepresentation overlap R hypergeometric

updated 4 months ago by ATpoint ★ 2.1k • written 4 months ago by charles.foster ▴ 140

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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…

Answer: log2 of normalized counts for further analyzes by James W. MacDonald 62k

This is covered in the [vignette][1]. [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#…

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Popular Question to Guido Hooiveld ★ 3.5k

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