Bioconductor BulkRNA-seq

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surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq

updated 6 months ago by jessica.anderson ▴ 10 • written 7 months ago by BioinfGuru ▴ 70

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Normalization BulkRNA-seq DESeq2

updated 4.1 years ago by Michael Love 43k • written 4.1 years ago by K. • 0

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Answer: Plot title for PCA in DESeq2 by ATpoint ★ 4.7k

The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.

Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0

I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…

Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k

VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…

Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k

It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…

Comment: WGCNA by pammelala304 • 0

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Answer: normalizatino of dna methylation EPIC data

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