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Wendy Qiao
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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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James W. MacDonald
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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…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species
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Benjamin
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I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot
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Guido Hooiveld
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4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species
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Mike Smith
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6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
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