Anyone use or have any background that you guys use on the regular basis? I have some RNA-Seq data which I am trying to learn some DESeq2. This has nothing to do with microbiome data, but some RNA-Seq data from some mice. Ben
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I really like the Phyloseq DESeq2 tutorial. He’s using DESeq2 on amplicons, but the same ideas apply for transcriptomics. This tutorial is short and sweet.
Of course the official DESeq2 vignette is the best guide. It discusses important diagnostic like the dispersion plots to make sure the test assumptions are valid.
Colin
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Thanks, yes, I was trying to add metadata to a data frame, but there’s some quirk to it as the metadata is a weird object, I ended up copying data into a column and it solved my problem. Thank you much. Ben
edit: https://support.bioconductor.org/p/110033/
was an interesting thread and gave me a lot of insight into the objects created by DESeq.
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