Bioconductor Rory Stark

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diffbind chipseq atac-seq rory stark

updated 6.5 years ago by Rory Stark ★ 5.0k • written 6.5 years ago by andrew.gehrke • 0

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diffbind rory stark

6.2 years ago andrew.gehrke • 0

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Rory Stark diffbind TMM edgeR chipseq

updated 7.2 years ago by Rory Stark ★ 5.0k • written 7.4 years ago by akdess • 0

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CHIPQC Diffbind chipseq rory stark Thomas Carroll

updated 13 months ago by arisarkar88 ▴ 40 • written 3.4 years ago by bioinfouser2 ▴ 10

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rory stark

6.8 years ago • updated 6.3 years ago mforoo1 • 0

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diffbind rory stark chip seq

updated 2.9 years ago by Rory Stark ★ 5.0k • written 3.4 years ago by bioinfouser2 ▴ 10

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diffbind Rory Stark coordinate

updated 3.5 years ago by Rory Stark ★ 5.0k • written 3.6 years ago by Guandong Shang ▴ 40

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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.

Comment: collapseReplicates error after tximeta by Michael Love 40k

A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…

Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

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Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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