I just came back from our Bioinformatic group (a rather loose association of various researchers at UofL interested in and doing bioinformatics) journal club, where we discussed this recent paper:
Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
Besides the catchy title that makes one believe that perhaps Google is getting into cancer research (maybe they are and we don’t know it yet), there were some interesting aspects to this paper.
What? For those who don’t know, CDF files are chip definition format files that define which probes belong to which probesets, and are necessary to use any of the standard summarization methods such as RMA, and others.
Why? Because we can, and because custom definitions have been shown to be quite useful. See the information over at Brainarray.
Why not somewhere else? A lot of times other people create custom CDF files based on their own criteria, and make it subsequently available for others to use (see the Brainarray for an example of what some are doing, as well as PlandbAffy)
TL;DR If you use the docopt package to create command line R executables that take options, there is something to know about numeric command line options: they should have as.double before using them in your script.
Setup Lets set up a new docopt string, that includes both string and numeric arguments.
" Usage: test_numeric.R [--string=<string_value>] [--numeric=<numeric_value>] test_numeric.R (-h | --help) test_numeric.R Description: Testing how values are passed using docopt. Options: --string=<string_value> A string value [default: Hi!