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addPatternDensity in 'qsea' takes too much time
MBD-seq qsea BiocParallel
updated 16 months ago by ▴ 220 • written 16 months ago by • 0
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Analysis of MBD-seq data without ssl control using BayMeth
Baymeth methylation MBD-seq Repitools
5.9 years ago pm2015 • 0
2 results • Page 1 of 1
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Answer: how to understand cpm=1 and how filterByExpr works? by gowthamee • 0
I found the following two articles very helpful in explaining the functions "cpm" and "filterByExpr" Article#1: From reads to genes to pat…
Comment: different results in DESeq2 when comparing groups in two ways by zohreh.fazelan • 0
Thank you for your response. But I have few comparisons in which there are more significantly expressed genes in the socond way compared to…
Comment: lmFit, continuous exposure, adjustment covariates by Gordon Smyth 45k
Your code `t(dat[43:ncol(dat)]` is not even syntactically correct. It could not possibly run in R. You need to create an expression matrix…
Comment: Handling of missing values in limma by Gordon Smyth 45k
limma uses all the observations. There's nothing complicated about it. limma does not remove any persons from the analysis. I did not tel…
Answer: after calcNormFactors with EdgeR, how to get TMM normalized matrix? by Gordon Smyth 45k
There's no such thing as a "TMM normalized matrix" or "normalized values" in edgeR. Have you read the edgeR User's Guide for how analyses a…
Votes
Answer: Using featureCounts and downloading Rsubread
Answer: different results in DESeq2 when comparing groups in two ways
Comment: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
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