Bioconductor Rnaseq

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limma limma voom rnaseq_analysis DEG

7.0 years ago • updated 6.0 years ago SPbeginner • 0

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rnaseq_analysis KEGG nonmodel species

updated 6.5 years ago by James W. MacDonald 68k • written 6.5 years ago by laural710 • 0

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sequencing rnaseq_analysis

7.2 years ago alemutak • 0

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rnaseq_analysis

7.8 years ago fakhter1 • 0

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rnaseq_analysis

updated 8.5 years ago by Gordon Smyth 52k • written 8.5 years ago by kjo ▴ 70

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deseq2 rnaseq_analysis variancestabilizingtransformation confounders

updated 8.8 years ago by Michael Love 43k • written 8.8 years ago by ompandey ▴ 10

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limma RNAseq_Analysis model.matrix

updated 9.8 years ago by Aaron Lun ★ 28k • written 9.8 years ago by anver • 0

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Comment: Annotation package for Manduca sexta by GA ▴ 10

Thank you!

Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

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Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

A: Is logFC a log2 fold change or some other base in scran::findMarkers

Comment: Error in retrieving clinical data

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