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Comment: Limma trend with limpa by Alejandro • 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error by asafpr • 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply! There are some pretty big discrepancies in the total raw counts between samples: ![enter image description here…
Answer: Limma trend with limpa by Gordon Smyth 52k
Dear Alejandro, Thanks for your interest. No, one does not set `trend=TRUE` when running eBayes() after dpcDE(). The variance trends are …
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
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Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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