Bioconductor Bulkrna-seq

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surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq

updated 16 months ago by jessica.anderson ▴ 10 • written 17 months ago by BioinfGuru ▴ 70

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Normalization BulkRNA-seq DESeq2

updated 4.9 years ago by Michael Love 43k • written 4.9 years ago by K. • 0

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Comment: GOseq Probability Weight Function bad fit by ejasge.r.m • 0

When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k

It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …

Comment: problem reading bam files into nucleR by efoss ▴ 10

I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…

Answer: two questions about limma by Gordon Smyth 53k

Answered here: https://support.bioconductor.org/p/16318/

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