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Comment: Remove duplicate genera in DEseq output? by Lluís Revilla Sancho ▴ 710

How is your data before calculating the deg_DESeq? I see you use `phyloseq_to_deseq2` which should work well, but have you double checked t…

Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat by Anna ▴ 20

Dear Gordon , Thank you very much I will do as you suggested When analyzing other data (like with normally distributed errors) is standa…

Answer: Interpret plot from DiffBind by Rory Stark ★ 4.8k

This plot has two columns, one for diseased (plotted in magenta) and one for control (plotted in purple) samples. There are two sets of pea…

Comment: DiffBind - Retrieving the differentially bound sites - HOW to calculate fold-cha by Rory Stark ★ 4.8k

Are you confident that in the non-control condition there is not a systematic loss of binding levels reflecting a true biological signal? I…

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…

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Answer: Interpret plot from DiffBind

A: VariantAnnotation non-model species

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Teacher to deeenes ▴ 30