Improved precision using updated probe set definitions. (A) We compared the precision in microarray experiments when using the updated probe set definitions in comparison with the original probe set definition (netAffx). We measured the precision as the Pearson correlation between two log2 ratios of expression levels generated by comparing duplicate sample-vs-control comparisons. The measurement indicates how well a fold change can be reproduced. Data from five different data sets generated using identical samples (data normalized using RMA) were averaged (mean) [see Additional file 1] for similar figures for each laboratory independently). The x-axis shows the number of probes integrated into each probe set. We grouped the number of probes into intervals of three in order to obtain a sufficiently large number of probe sets to get a robust estimate of each data point. The y-axis shows the mean correlation/precision across the five labs for each interval. (B) Visualizing the number of probe sets in each interval between the different probe set definitions.