Microarray Analysis Open Software
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14.7 years ago

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?

open-software microarray-analysis • 3.3k views
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14.7 years ago
Paulo Nuin ★ 3.7k

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

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

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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/

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We too had good experience with this package ++

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@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?

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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

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

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14.7 years ago
Ljxue ▴ 10

Tigr MEV, very useful.

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13.9 years ago
Dejian ★ 1.3k

limma, or visit Using Bioconductor for Microarray Analysis

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