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DESeq2 l

updated 7 months ago by Michael Love 40k • written 7 months ago by Paula • 0

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l DESeq2

updated 21 months ago by ariel ▴ 10 • written 2.0 years ago by aedavids ▴ 20

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MEDIPS edgeR l

2.0 years ago Aranzazu • 0

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TCGAbiolinks data normalize l

updated 2.2 years ago by Kevin Blighe 3.8k • written 2.2 years ago by DANIELA • 0

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Answer: shinyMethyl - saving the file by Guillaume Devailly ▴ 60

You can probably save individual plots by right-clicking on them an save individual images. Maybe printing the page as a pdf will also work…

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…

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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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