Alternatives To Caarray For Microarray Storage
Entering edit mode
13.9 years ago

Our lab has generated several microarray data sets a year (50-100 samples per experiment), and is about to start generating a whole lot more. I need an organized way to store and retrieve Affymetrix CEL files (SNP and gene arrays) and Illumina raw data and the normalized versions of those data. I will need to store on the order of thousands of arrays. The software should be free and should run on a standard linux stack. I do not need a fancy integrated analysis factory on top of the storage. I am only solving this problem for my own lab, not for my whole institution.

caArray is an obvious choice. With caArray I get standards compliance (good practice, and good for NIH grants which ask how you'll use their tools) and what looks from the outside like a mature product. Can anyone with personal experience (meaning that you have installed and actually use the product yourself) recommend an alternative to consider in a bake-off? Thanks.

microarray data • 2.8k views
Entering edit mode
13.8 years ago
Paulo Nuin ★ 3.7k

I think you need BASE

BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.

Just adding, we use BASE to store some of our data and it very well.

Entering edit mode

I had forgotten all about BASE; I remember the buzz around it when it was first released, maybe 7-8 years ago? It is a good alternative.

Entering edit mode

It's still under development and well maintained. We use with a backend on Postgres, much better than MySQL.


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