Bioconductor DEAnalysis

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DEanalysis limma olinktargetedproteomics

updated 7 hours ago by Gordon Smyth 52k • written 1 day ago by svlachavas ▴ 840

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FPKM RNASeqData DEAnalysis limma

17 months ago Ethan Nguyen • 0

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edgeR deanalysis test fisher exact

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.0 years ago by thkapell ▴ 10

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edgeR rnaseq DEanalysis TCGA independent filtering

7.2 years ago svlachavas ▴ 840

4 results • Page 1 of 1

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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

Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.

Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380

Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…

Comment: normalizatino of dna methylation EPIC data by user_bioinfo • 0

yes actually that's why I did, and its all good! thank you for your response

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Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu

Answer: normalizatino of dna methylation EPIC data

Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

Suggesting changing the "reply-to" field to the mailing list address.

Answer: UniProt.ws query for single UniRef90 ID takes several minutes

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