Daily Archives: November 7, 2007

Data clustering with Python

November 7, 2007 – 19:15

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.

Read More »

By Einar | Posted in Linux, Science | Tagged , , , | Comments (1)

Buggy bioinformatics software

November 7, 2007 – 15:43

As people who read my science-related posts know already, I’m not a big fan of software made just to support a publication. Recently I’ve stumbled again into similar software. Namely, I’m talking about the TIGR Multiexperiment Viewer (TMeV), a Java-based program which is often used for microarray analysis. It’s not exactly “fit for publication”, because it has reached version 4 last year, but shows some of the problems (mentioned already) with releasing bioinformatics software.

I use TMeV mostly because I didn’t find any other implementation of the hierarchical clustering algorithm with support trees. However, I’ve stumbled upon a very annoying bug in the most recent version. Normally I use average linkage clustering and as the distance metric I employ the Pearson’s correlation, and with gene and sample bootstrapping: with certain files this makes TMeV report errors at random during the iterations.

Read More »

By Einar | Posted in Linux, Science | Tagged , , , | Comments (0)