Bioconductor Contrastmatrix

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edgeR contrastmatrix limma

updated 1 hour ago by James W. MacDonald 68k • written 23 hours ago by Elizabeth • 0

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champ bioconductor contrastmatrix compare.group

updated 6.2 years ago by Yuan Tian ▴ 290 • written 6.2 years ago by erinkello • 0

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Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by aitor • 0

Hi everyone. I have a RIP-Seq analysis with 3 conditions and 3 assays (IP, IgG and Input for each of them). 4 replicates for each conditio…

Comment: Discrepancy between Excel TPP-TR reported values and the Melt Curve reported val by James W. MacDonald 68k

You will need to provide a self-contained example, or it is unlikely that anybody could debug any possible issue.

Answer: Limma - Complex 2-way multi-level contrast with paired samples by James W. MacDonald 68k

If you are fitting donor as a fixed effect you do not also need to fit as a random effect. The limma package fits a generalized least squar…

Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.7k

Yes, perfectly valid. Analyzing counts from high-throughput experiments with DESeq2 (or edgeR, or limma) is standard. After all, what DiffB…

Comment: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf by AB ▴ 110

Force=TRUE did the trick. Thank you.

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