biomaRt and GenomeGraphs: a worked example

As promised a few posts ago, another demonstration of the excellent biomaRt package, this time in conjunction with GenomeGraphs.

Here’s what we’re going to do:

1. Grab some public microarray data
2. Normalise and get a list of the most differentially-expressed probesets
3. Use biomaRt to fetch the genes associated with those probesets
4. Plot the data using GenomeGraphs

If you want to follow along on your own machine, it will need to be quite powerful. We’ll be processing exon arrays, which requires a 64-bit machine with at least 4 GB (and preferably, at least 8-12 GB) of RAM. As usual, I’m assuming some variant of Linux and that you’re comfortable at the command line.