Bioconductor Gene expression

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gene expression network cytoscape

7.2 years ago torgeirous • 0

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limma gene expression confounding adjustment paired

9.4 years ago Loodramon • 0

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sva combat gene expression batch effect rnaseq

updated 9.6 years ago by Jeff Leek ▴ 650 • written 9.6 years ago by Farshad Farshidfar ▴ 10

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ggplot2 barplot gene expression gene expression

updated 9.7 years ago by James W. MacDonald 68k • written 9.7 years ago by alakatos ▴ 130

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Comment: Differential expression analysis using two TCGA datasets by ATpoint ★ 4.8k

If these are two different batches then they're fully confounded making it statistically invalid. Biologically, I find it at least question…

Comment: PhD scholar by ATpoint ★ 4.8k

Hi, please consider asking this at biostars.org as here we're mainly answering precise technical questions towards the packages. You are se…

Answer: how to use `arrayWeightsQuick()`? by Gordon Smyth 52k

Yes, that is the correct way to use `arrayWeightsQuick`. Thanks for pointing out that there is still a reference to `arrayWeightsSimple` i…

Answer: fast apply on RleList by story.benjamin ▴ 20

solved with viewApply (code is simplified below) + map reduce on chrs test.split <- split(test.gr,seqnames(test.gr)) final.st…

Comment: fast apply on RleList by story.benjamin ▴ 20

Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…

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Having Trouble Using CNE12() and CNE21() in CNEr

Answer: Having Trouble Using CNE12() and CNE21() in CNEr

annotation EpicV2

Answer: fast apply on RleList

Answer: BiocParallel_1.40.1.tar.gz not available

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Popular Question to Ariel Chernomoretz ▴ 170