Scatter plots of residuals for versus log(3) as independent variables together with various STIs

Abstract

Copyright information: Taken from Exploratory differential gene expression analysis in microarray experiments with no or limited replicationGenome Biology 2004;5(3):R18-R18.Published online 1 Mar 2004PMCID:PMC395768.Copyright © 2004 Loguinov et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. Residuals for artificial data drawn from a bivariate normal distribution with the same parameters as the real data shown below. This plot is based on the same simulated dataset as in Figure except that the linear trend has been subtracted resulting in slope = 0. A robust scale estimator (a Huber -estimate of scale) for residuals (green, outer), (purple, middle) and -based (orange, inner) scale estimators are shown. Scale factors calculated to adjust - and -based scale estimates were 1.25 and 1.35, respectively. Adjusted -based STIs for the real data at the 95% (innermost), 99%, 99.8%, 99.98% and 99.998% (outermost) levels. These adjusted STIs take into account differences between the ordinary STIs and -based STIs for an artificial dataset having the same parameters (location, scale and coefficient of correlation) as its cognate real data. The vertical dotted line marks the location of the minima of the empirical hyperbolas. Red or pink and blue or cyan dots correspond to up-regulated and down-regulated genes, respectively, with -value ≤ 0.01 (≤ 0.05). The most prominent down-regulated gene with case index number 4,301 is Mac1 (see also Table ), which is not expressed in the strain.