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.