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Answer: DESeq2 parameter infernce by Michael Love 39k

We use IRLS which is related to Newton-Raphson method. I suppose you can use any optimization method you prefer. We also sometimes use L-BF…

Answer: DESeq2 with 2 continuous factors, LRT, coeficients and slope by Michael Love 39k

See `?results` which describes what the LFC is when you perform an LRT: "*For analyses using the likelihood ratio test*..." Also in the …

Answer: DESeq2 with sample effect, unequal sample sizes by Michael Love 39k

For statistical analysis plans such as design and coefficient interpretation, I recommend collaborating with a local statistician or someon…

Comment: Bioconductor tool for curating annotations? by Lluís Revilla Sancho ▴ 700

I think you can find those transcripts not overlapping with a GRanges object easily via ?GenomicRanges::setdiff, but I don't know how to an…

Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by drknwk • 0

Exact same problem here suddenly. Hope someone will have a fix soon!

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Answer: Limma-voom with inverse probability weights

A: Limma-voom with external observation weights

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