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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?
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Eva
▴ 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
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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 …
Comment: Are transformed values from rlog /vst log2 normalized counts?
by
James W. MacDonald
67k
The `DESeq2` package is meant to analyze count data! Most packages that are intended to be used for RNA-Seq data are going to want the raw …
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Answer: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Unable to install any Bioconductor package with new R 4.4.1 - path nor writable
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
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