Biostar Time series analysis

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edger Time series analysis

updated 2.4 years ago by Gordon Smyth 47k • written 2.4 years ago by josmantorres ▴ 10

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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…

Comment: Combat and dds Object by ATpoint ★ 2.1k

I cannot reproduce this, please provide a minimal reproducible example. This here works just fine: ```r library(DESeq2) library(sva) dd…

Comment: pathview says my nonmodel species is unknown: "species invalid" by nute11a • 0

Restarting R worked :) thanks!!

Answer: Different summary() and results() values in DeSeq2 by swbarnes2 ★ 1.2k

211k genes? That's a lot. It looks like the difference is in the gene filtering. The top one is filtering way genes with a mean counts <…

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Popular Question to Guido Hooiveld ★ 3.5k

Scholar to James W. MacDonald 62k

Commentator to Michael Love 39k