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Answer: How to subset voomLmFit (MArrayLM) object?
by
Gordon Smyth
51k
Yes, the current behaviour is absolutely intentional. It doesn't seem to me to be meaningful or useful to try to subset the EList object au…
Answer: Need help interpreting heatmaps from limma
by
James W. MacDonald
67k
Heatmaps don't do any comparisons. They just plot the underlying data in a matrix and color the blocks based (in your case) on the by-gene …
Comment: Are transformed values from rlog /vst log2 normalized counts?
by
Eva
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10
I understood exactly what you said, but I got confused with the documentation and the info that gives about rlog because it seems to be tha…
Answer: featureCounts fails to load annotation file
by
James W. MacDonald
67k
I imagine Wei Shi will be along later with actual help, but for now do note that you can use an SAF file instead of a GTF. It's easy enough…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
67k
That error indicates that you have a file called NCBI.sqlite in your working directory that is missing some tables. You should delete that …
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