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public data TCGA GTEx Tutorial

7.3 years ago shepherl 4.1k

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Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.

Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.

Comment: Differential Expression Genes as Independent Variables by abadgerw • 0

The data that is repeated is a quantitative metric of post-mortem pathology across multiple sections. Not all patients have the same number…

Answer: Crossover design with limma by Gordon Smyth 52k

Your experiment is somewhat more elaborate than a classical crossover design because of the period-specific baseline controls. The analyses…

Answer: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Sorry, your question doesn't make sense to me. There are tens of thousands of genes and you can't run a mixed model analysis with one depen…

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