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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder
by
ATpoint
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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
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Mike Smith
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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
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Gordon Smyth
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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
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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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