Figure 1.

(a) Fluorescence image of a hybridized Affymetrix GeneChip Mouse Genome MG430 2.0 array (GEO GSE12545). The chip surface divides into a grid of nearly 10⁶ fluorescing probe spots. The bright horizontal stripe matches with probes the 25meric sequence of which starts with triple degenerated guanines ((GGG)₁-motif). Triple runs of other nucleotides are not associated with bright stipes. The position of the respective probes are shown at the rigth border of the figure. (b) Boxplots of expression measures obtained from the intensity data shown in panel a using various preprocessing methods (see text for assignments). The boxplots are computed separately for all probe sets (45,100) and for probe sets with at least two probes containing the (GGG)₁-motif (836, i.e. 2% of the total number). 'log I' denotes the distributions of raw intensity data. Note that essentially all methods except Plier and partly mas5 are unable to correct expression values for the (GGG)₁-bias. The respective distributions of probe sets containing (GGG)₁-probes are systematically shifted towards larger expression values compared with the distribution of all probe sets.