Scatter plots of log
array-mean-centered PM probe intensities vs. PM probe affinities. The top row shows scatter plots for all four arrays (A,B,C,D) for Hsbp1, the number 1 up-regulated gene. The bottom row shows all four arrays for gene Id2, the top down-regulated gene. Affinities explain only a small part of variation between probes at the gene level. Affinities were calculated using the default method in Bioconductor package gcrma version 2.20. Affinities for perfect match probes are shown. Pearson correlation coefficients vary from 0.08 to 0.76 on the 8 scatter plots above. A scatter plot of affinities vs. log2 probe intensities (not shown) for all probes in array C are similar to the corresponding diagram in Wu et al. .