Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays

A few years ago I was involved in analysing some time-course microarray data. Our biological collaborators were interested in how we analysed their data, so this lead to a creation of tutorial, which in turn lead to a paper. When we submitted the paper, one the referees “suggested” that we write the paper using Sweave; I had never used Sweave. At the time this was a massive pain and I regularly cursed the name of the anonymous referee.  A few years later, I’ve just updated code (due to a change in Bioconductor) and it was a breeze. A belated thanks to the referee.

In this latest update to the paper I’ve

• moved the paper to github;
• changed from Sweave to knitr;
• used RStudio instead of emacs.

You can find details full details about analysis on the associated github page.