Question: Microarray Analysis Open Software
1
gravatar for Eric Normandeau
9.3 years ago by
Quebec, Canada
Eric Normandeau10k wrote:

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?

software open analysis microarray • 2.0k views
ADD COMMENTlink modified 8.5 years ago by Dejian1.3k • written 9.3 years ago by Eric Normandeau10k
4
gravatar for Paulo Nuin
9.3 years ago by
Paulo Nuin3.7k
Canada
Paulo Nuin3.7k wrote:

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

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

ADD COMMENTlink written 9.3 years ago by Paulo Nuin3.7k
2

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/

ADD REPLYlink written 9.3 years ago by Michael Kuhn5.0k

We too had good experience with this package ++

ADD REPLYlink written 9.3 years ago by Istvan Albert ♦♦ 80k

@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?

ADD REPLYlink written 9.3 years ago by Eric Normandeau10k

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

ADD REPLYlink written 9.3 years ago by Paulo Nuin3.7k

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

ADD REPLYlink written 9.3 years ago by Paulo Nuin3.7k
1
gravatar for Ljxue
9.3 years ago by
Ljxue10
Ljxue10 wrote:

Tigr MEV, very useful.

ADD COMMENTlink written 9.3 years ago by Ljxue10
1
gravatar for Dejian
8.5 years ago by
Dejian1.3k
United States
Dejian1.3k wrote:

limma, or visit Using Bioconductor for Microarray Analysis

ADD COMMENTlink written 8.5 years ago by Dejian1.3k
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