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SummarizedExperiment vignette

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vignette

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Answer: EdgeR: Exact test and glmQLFTest produce very different results by James W. MacDonald 64k

You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.

Answer: limma::voom vs edgeR::voomLmFit - when to use? by James W. MacDonald 64k

The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…

Comment: 'Subtracting' counts on basis of Negative control media and water samples by Karthik • 0

I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…

Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k

It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…

Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor by arina • 0

Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …

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A: DSS understanding delta option and posterior probability

Comment: Ensembl down???

Answer: How should I run ssGSEA Hallmark Enrichment Analysis?

Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default

Comment: Problem loading HDF5Array in R 4.3.2

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Popular Question to Endre Sebestyén ▴ 70