After a bumpy road, along which I kept in mind Jeff Leak’s own worst (recent) experience, we finally got our article on Time-Course Gene Set Analysis for Longitudinal Gene Expression Data published in PLoS Computational Biology, a very nice journal ! I am really happy about it, don’t hesitate to check it out ! And there is the TcGSA R package that goes with it.
This is a quick technical post, that is as much about disseminating the information as putting it in a place where I can find it again in the future. I have been trying to use openMP in an R package that I am currently developing. OpenMP is supported by the popular gcc compiler. However, OS-X Xcode now ship with a clang compiler that does not support openMP. So first one needs to install gcc (from homebrew for instance). The thing is then to get R to actually use this gcc compiler. After many hours of struggle, I got it working by modifying the “~/.R/Makevars” file, in which clang must be replaced by gcc (or gcc-$version).
In the case where there is no .R folder and/or Makevar file, just create one. In order to replace clang by gcc, the two following lines suffice:
gcc-4.9 can of course be replace by any other compiler you might want to use ( such as another version of gcc for instance), and an absolute path to the compiler can also be specified (see comment from kamvarz below)
On March 6th, 2015, I defended my thesis in front of a prestigious jury, and was awarded the title of Ph.D. in Public Health with a concentration in Biostatistics (Docteur en Santé Publique — option Biostatistique) from the University of Bordeaux. After more than 3 years of hard work, that’s an incredible feeling. For the interested reader, My Ph.D. thesis !
I am in the process of speeding up some code, and I have been lured by the promises of Rcpp. Since the functions I am working on are mainly linear algebra, I wanted to try out RcppArmadillo. This put my googling skills to a test as I spent (way) too much time trying to figure out errors until I found this post. Thank you James Balamuta ! Be warned RcppArmadillo, microbenchmarking is on !
The American Statistical Association launched a new website thisisstatistics with general information on what being a statistician really means today. I often meet fearful looks when I meet people and present myself as a “biostatistician” (the key word being statistician here). Up to the point that I now generally say I work in “applied mathematics in medicine”, before I drop the magical “big data” keyword in the necessary explanation following this title.
This website seems very easy to navigate, and I hope it will participate in the heat statistics are getting, being the sexiest job this days !
Check out the 2 short videos below: