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. So I turned to R, which offers a GEO query module through Bioconductor.
Again that proved to be a terrible mistake. For a file containing 183 samples, the analysis is going on since four hours and with no sign of completing anytime soon (not to mention a possible memory leak). After this, I gave up. I’m going to get the reduced data sheet and write a small parser in Python myself.
What is frustrating is the lack of quality: I could concentrate on my own work rather than reinventing the wheel for the nth time if the existing implementations worked. What’s the point in releasing non-working software? I could understand bugs, but this is one step further.
Today I was looking for an easy way to do some calculations of raw expression data on Affymetrix arrays, but I didn’t want to use R: I have already mentioned how I don’t like its design and implementation. While looking for some documentation, I stumbled upon this nifty little program called RMAExpress.
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December 27, 2005 – 13:52
Name: Luca Beltrame
Location: Milano, Italy
Birth date: September 6, 1977
Occupation
I am a biotechnologist. I started working “at the bench”, first with biochemistry then with cellular biology. After two years of bench work, I’ve moved to bioinformatics, and in particular to analysis of microarray data in cancer research studies. My current interests are neuroscience and the application of group testing techniques to genome-wide transcriptomic profiling.
I am currently working as a research fellow at the Institute for Biomedical Technologies, a department belonging to the CNR (Consiglio Nazionale delle Ricerche), while doing a Ph.D. in Molecular Medicine for the University of Milano. My work place is the Centre of Excellence CISI.
For those interested, you can view my resume.
