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Answer: Handling NA's in Deseq2 by ATpoint ★ 2.9k

DESeq2 objects are SummarizedExperiments and these follow standard R rules. If you had an object `dds` with a column `group` then you wo…

Comment: S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconduct by Marshall • 0

@[avatar game][1] Thanks for support. [1]: https://avatargame2.com

Answer: Use with_go along with other filters in getBM function by Mike Smith ★ 6.0k

You hit on the right solution with your final example. Here's a slightly modified version where I've given names to the list elements in `…

Comment: Can VST-transformed community composition data be expressed as relative abundanc by dwas • 0

Thank you for your fast and helpful clarifications. I must have understood the pseudo-counts wrong (the video episode CC195 of the Riffomo…

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Gordon Smyth 47k

limma already adjusts for the baseline expression level of each subject. Trying to include baseline expression explicitly in the linear mod…

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A: VariantAnnotation non-model species

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