We too had good experience with this package ++

@nuin Thanks for the answer! Looks promising, I'll dig into it some more. For the benefice of other users, maybe you can describe the software a bit and tell about it's strong and weaker points?

MEV is a complete microarray package that is able to handle a myriad of file formats and has several algorithms for analysis, normalization, visualization, among other things. I haven't used it for some time already (we have proprietary tools now) so I cannot say for sure about strong and weak points wit confidence. Anyway, the pros are 1) handles any type of data, 2) cross-platform java application, 3) many analytical options. Cons are 1) sometimes your file format might not be recognized and you would need to work on your inputs, 2) java is sometimes slow

(less now, I think) and 3) too many analytical options.

depending on the annotations you use for your array, you can also use Gaggle to send data from MeV to other tools, e.g. David and STRING: http://gaggle.systemsbiology.net/