Microarray Analysis Open Software

Question

[Eric Normandeau]

What open software have you used for microarray analysis?

I am using custom made arrays and can easily extract matrices of gene expression levels for each individual and each gene.

I am looking for a replacement for the R-maanova package that we have been using for years now in the lab, but given our good experience with this one, I don't want to waste time trying to learn an only half-assed solution. :)

So, what have you used that you would unconditionally recommend?

Answer 1

[Paulo Nuin]

http://www.tm4.org/mev/

That's basically all you need for custom made arrays.

[Michael Kuhn]

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/

[Istvan Albert]

We too had good experience with this package ++

[Eric Normandeau]

@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?

[Paulo Nuin]

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

[Paulo Nuin]

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

Answer 2

[Ljxue]

Tigr MEV, very useful.

Answer 3

[Dejian]

limma, or visit Using Bioconductor for Microarray Analysis