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Answer: AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site) by James W. MacDonald 62k
Try setting `options(timeout = 5000)`
Answer: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE by vs2001 ▴ 40
Apparently, UCSC changed their assembly again. See the discussion on the [Bioconductor/GenomeInfoDB][1] Github page. The solution is explai…
Answer: msPurity::spectralMatching Error in getSmeta(con, pids) : No meta data for spect by thomas.nigel.lawson • 0
This has been resolved (Windows Firewall issue) - see github issue https://github.com/computational-metabolomics/msPurity/issues/100
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 …
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Answer: AnnotationForge::makeOrgPackage "argument is missing, with no default" Errors
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Comment: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
Answer: Limma-voom with inverse probability weights
A: Limma-voom with external observation weights
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