Bioconductor Relevel

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deseq2 lfcshrink relevel

updated 5.9 years ago by Michael Love 40k • written 5.9 years ago by mat.lesche ▴ 90

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junctionseq relevel reference

6.6 years ago Assa Yeroslaviz ★ 1.5k

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junctionseq qorts multiple factor design relevel

6.6 years ago Assa Yeroslaviz ★ 1.5k

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deseq2 relevel resultsNames multifactorial design

updated 7.6 years ago by Michael Love 40k • written 7.6 years ago by rclaire ▴ 20

4 results • Page 1 of 1

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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 …

Votes

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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