So I'm currently interested in playing with inferring gene regulatory networks from microarray data. I've downloaded a longitudinal study from GEO and I'm playing with various available BioC packages out there. I was wondering what kind of pre-processing people use/recommend for this kind of task. I've done lots of differential expression kind of things, but have no experience with this.
Are there a different set of protocols / methods for this? Which normalisation method would people recommend?
UPDATE: So Will kind of answered this a while ago. I was wondering if anyone had anymore suggestions: for example in this paper biomedcentral.com/1752-0509/1/37 they remove probes with a maximum intensity value < 5 . All of these thresholds seem arbitrary to me and a bit rubbish. Any more comments / ideas greatfully recieved. I m not sure of the proper etiquette to re-open a question.