I try to use FOSS extensively for my scientific work. In fact, when possible, I use only FOSS tools. Among these there is the R programming language. It’s a Free implementation of the S-plus language, and it’s mainly aimed at statistics and mathematics. As the people who read my scientific posts know, I don’t like R much. But sometimes it’s the only alternative.

Well, what does R have to do with KDE? With this post I’d like to start a series (hopefully) of articles that deals with KDE programs used for scientific purposes. In this particular entry, I’ll focus on rkward, a GUI front-end for R.

I’m often wondering why people only resort to R when working with microarrays. I can understand that Bioconductor offers a plethora of different packages and that R’s statistical functions come in handy for many applications, but still, I think people underestimate the impact of performance. R is not a performing language at all, it doesn’t parallelize well when using HPC (at least from the talks I’ve had with people studying the matter), and in general is a memory and resource hog.

**Notice:**Just now I realized this has been linked to to a Stack Overflow question. I recently wrote a new post that uses a different technique and a combination of R and Python. [Check it out!]({{ site.url }}/2011/05/multiscale-bootstrap-clustering-with-python-and-r)

Following up my recent post, I’ve been looking for alternatives to TMeV. So far I’ve found the R package pvclust and the Pycluster library, part of BioPython. The first one also performs bootstrapping (I’m not sure if it’s similar to what support trees do, but it’s still better than no resampling at all). I’ve found another Python project but it is still too basic to perform what I need.

Today I started working on a data set published on GEO. As the sample data were somehow inconsistent (they mentioned 23 controls when I found 28), I decided to parse the SOFT file from GEO in order to get the exact sample information. I did a grave mistake. First of all, Biopython’s SOFT parser is horribly broken (doesn’t work at all) and quite undocumented: I could work around the lack of documentation (API docs) but not with the fact that it wouldn’t work.