How to create interaction networks from Agilent microarray data?

Question

[ccarril]

Hi everyone

Who create interaction network from (with Cytoscape, TM4, R or another free software) from data of agilent microarray?

Is exist a protocol for it?

Thanks

[ccarril]

But, when I need to make this kind of graphic, What type of data I need to extract from .txt file (agilent format from microarray) to make this graphic?

[SP]

Normally you need a text file with column probe-id, and respective intensity for each probe.

e.g. ProbeId, sample1, sample1, sample1, sample2, sample2, sample2

Answer 1

[SP]

If you want to create co-regulation network you can use biolayout http://www.biolayout.org/. It also uses ML clustering for clusters. You can use those sub network in cytoscape as well.