Alternatives To Caarray For Microarray Storage
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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
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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.

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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.

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

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