Standard error as a function of the difference in means. Shown is σ2 as a function of (see Equation 1 in the text) for probes from null genes from the comparison of Latin Square experiments 1 and 2 for (a) all approximately 500,000 probes on the array, (b) approximately 22,000 probes after RMA summation but in the absence of quantile-quantile normalization, and (c) after background correction, quantile-quantile normalization, and RMA summation. A small number of outlying data points are excluded from each panel. RMA, Robust Multichip Average.
Fodor et al. Genome Biology 2007 8:R69 doi:10.1186/gb-2007-8-5-r69