lumi **

Lumi is an ongoing project for Illumina microarray data analysis, including the design of a software package in R/Bioconductor and the discussion of microarray experiment design.

** an open source project at the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University.


SQLite on Mac/ Bioconductor

As our data set growing bigger and bigger, keeping them in a flat file is no longer possible.

I am looking for a database solution. SQLite is an obvious choice for two reasons:
1) Fast: It gains the speed by getting rid of the client/server mode of most databases.
2) Able to handle large (>> tera-tera bytes) data.

SQLite comes with a GUI interface

However, as with any other free stuffs, installing it on a Mac seems a challenge. My colleague pointed me to Darwinports, a program facilitating the installation and compiling.

With a few kinks, it works out.

Total time needed: 1 h. Total frustration: medium high.

On the Bioconductor side, RSQLite and DBI libraries are needed.


Post a Comment

<< Home