Hello:

What kind of clustering methods is suggested for gene expression data (two
color agilent) of disease and normal samples obtained from sampe patient.
Given all samples are of same phenotype, and genes obtained are
differentially expressed (20% FDR from limma) , will clustering really help.
What kinds of analyses a bioinformatician would suggest ( say, since all
samples of of same phoenotype clustering is not a indicative of class
identification.  Possibly gene clustering might suggest gene classes).
Also, what kind of parameters one should choose for clustering given paired
samples.
I appreciate your suggestions. Thanks
Adrian.

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