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RNA-Seq edger fitted values differential expression normalization

updated 3.6 years ago by Gordon Smyth 47k • written 3.6 years ago by David R ▴ 70

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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#…

Comment: mas5calls function doesn't work; mirna40cdf problem by James W. MacDonald 62k

Except that the miRNA arrays are sort of dumb. An miRNA is 21-23 nt long, and Affy probes are ... 25 nt long. So a 'probeset' for an Affy m…

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Popular Question to Guido Hooiveld ★ 3.5k

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