Bioconductor Gene set testing

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8.1 years ago • updated 8.0 years ago svlachavas ▴ 810

14 results • Page 1 of 1

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Answer: DESeq2 + analysis question for design with uneven time point design by Michael Love 40k

I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…

Answer: Genes with highest differential expression have very low read counts for most ge by Michael Love 40k

Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.

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

> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…

Comment: Extract Limma Adjusted Values for Plotting by ATpoint ★ 2.9k

Yes, with normalized counts on log2 scale.

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

A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…

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A: Ranges from a fasta file

Answer: NA transcript values in my Txdb

Comment: Interpret plot from DiffBind

Answer: Use with_go along with other filters in getBM function

Awards • All

Scholar to Mike Smith ★ 6.0k