Hi All,

I am trying to analyze expression array data (single color on Agilent
platform) from a disease scenario where we have 5 normal samples (untreated)
with 6 patients treated with drug A and 5 patients treated with drug  A +
B.  The biologists question is there any serious perturbations of the genes
between two groups (Treated with A only and treated with A+B). They are
interested to represent the same by a cluster.

I am just wondering, whether I should do separate analysis of those two
groups using limma and cluster together by selecting genes using some
parameters such as P value or fold value.?
or
Whether I should do analysis together using limma and cluster it by
selecting genes by fold value of P value.?

It will be of great help if any one of you could provide suggestions on the
same.

Thanks in advance.

Regards,
Abhilash

	[[alternative HTML version deleted]]

