 Dear List,

I am using affymetrix chip in a methodology. I want to know the repeat level
from duplicate or triplicate samples by reading chip results. any
suggestion? shall I use signal correlation coefficient? Or compare toptable?
any other better way? Basically, I have 2 samples in each situation.

Right now, I am comparing the toptables, produced by limma. It seems the
results sorted by "M", log fold change is reasonable to us. But I found,
there is better repeat level if I sorted by "B", the log odds ratio. Anybody
has this experience? and, could any one tell me what "B" really represent
and come from?

Thanks in advance,

Di Wu
Graduate student, Research Assistant 3
Department of Epidemilogy and Biostatistics, department of Pathology
Case Western Reserve University

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