Title: Direct versus indirect designs for cDNA microarray experiments
Authors: Terence P. Speed and Yee Hwa Yang 
Date: April 2002
Pub: PDF
Url: http://www.stat.berkeley.edu/users/terry/zarray/TechReport/616.pdf

Abstract:
We calculate the variances of two classes of estimates of differential
gene expression based on log ratios of fluorescence intensities from
cDNA microarray experiments: direct estimates, using measurements from
the same slide, and indirect estimates, using measurements from
different slides.  These variances are compared and numerical estimates
are obtained from a small experiment involving 4 slides. Some qualitative
and quantitative conclusions are drawn which have potential relevance to
the design of cDNA microarray experiments.