Recommend Easy To Use Microarray Clustering Software
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15.2 years ago

Feel free to post your favorite clustering tool.

microarray clustering • 11k views
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15.2 years ago

One of my favorites is the MEV micro-array data analysis tool. It is simple to use and it has a very large number of features.

Works well for any type of data. You can also load into it data from a file that is in a simple text format:

GENE1, value1, value2
GENE2, value1, value2

Feel free to post your favorite clustering tool.

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It used to be a Java application that ran without problems as long as Java was properly installed. Did the requirements change in the meantime?

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I just found that MEV was far from easy to install under linux.

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14.7 years ago
Stew ★ 1.4k

My favourite clustering software is R. Some people may disagree about the 'easy to use' part but once you get over the initial slope of the learning curve it is very easy and hugely powerful. No other tool can really compare in my opinion. However if R is not for you then Cluster 3.0 and MapleTree are the way forward.

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@Eric: Clustering algorithms in R are quite many. Try for example: example(kmeans).

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@Stew How is R a clustering software? What package or function do you use for clustering? Could you put a short example code here? Many thanks!

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14.8 years ago

I am currently using Cluster 3.0 for clustering and TreeView.

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15.1 years ago
Zhenhai Zhang ▴ 170

I would recommend a combination of cluster and treeview.

pretty powerful!

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14.8 years ago
Alex ▴ 190

Possibly related: http://mmc.gnets.ncsu.edu/

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14.8 years ago
Geoffjentry ▴ 320

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion.

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This would be my first choice as well.

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14.2 years ago
Rm 8.3k

I use TM4 MultiExperiment Viewer (MeV), SMD and Eisen's Cluster3 with treeview. MeV has more capabilities to handle the microarray data.

Microarray Resources : Software and Tools

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14.2 years ago
Puthier ▴ 250

You may also try EXPANDER and SEURAT

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12.7 years ago

One thing you might look at is the Broad Institute's genepattern software. It can be clunky at times but it will do most common tasks in a fairly straightforward fashion herve leger

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