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limma camera cameraPR edgeR gene set testing

updated 6.1 years ago by Gordon Smyth 51k • written 6.1 years ago by jamie.gearing ▴ 60

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Comment: Are transformed values from rlog /vst log2 normalized counts? by 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 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 …

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 …

Comment: Are transformed values from rlog /vst log2 normalized counts? by Eva ▴ 10

Many thanks for you detailed answer, I really appreciate it. Could you give me an example (or more if possible) of analysis using count-b…

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Scholar to James W. MacDonald 67k