Bioconductor Gene set

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Gene set gene set analysis omiccircos

updated 6.1 years ago by yifangt ▴ 20 • written 8.7 years ago by Peter.Wood • 0

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mroast roast gene set gene set analysis edgeR

updated 7.3 years ago by James W. MacDonald 63k • written 7.3 years ago by lattalic • 0

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GAGE gene set go.gsets

updated 3.1 years ago by Luo Weijun ★ 1.6k • written 3.2 years ago by June. ▴ 10

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globaltest gene set

6.8 years ago the_august • 0

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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 …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

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

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

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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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