[BioC] Best way of presenting a sub-fraction of edgeR RNAseq gene expression results in a publication

Sindre [guest] guest at bioconductor.org
Thu Jan 30 12:49:18 CET 2014

We selected a priori 5 genes to analyse and want to include them in a table for publication.

Question is how to present them? Normally we would calculate fold changes (or percent) with standard deviation and then mark if significant.

edgeR, as far as I understand, uses shrunken fold changes and the dispersion is squeezed using an empirical Bayes method. Thus, its hard to manually reproduce the results from logCPM values.

So, whats the best way?

Thank you!

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