Effects of probe number on the variation of gene expression scores. Median interquartile ranges (IQRs) of expression scores (Y-axes) for the indicated tissue from all humans and chimpanzees are plotted in red relative to the number of 1H_1C probes remaining in a probe set (X-axes). Median IQRs are plotted in black for simulated data wherein different numbers of probes were randomly sampled from 1H_1C_11 probe sets (see text for details). Note that only probe sets expressed in a given tissues are considered in this analysis (see Methods). Data from even (Panels A, C, E, G, and I) and odd numbers of remaining probes (Panels B, D, F, H, and J) in probe sets are presented separately due to inherent differences in the way the median polish algorithm employed by RMA processes them. Two-slope red and black lines are provided for the actual and simulated data, respectively (see Methods). The tissue from which the data was collected is indicated in each panel.
Toleno et al. BMC Bioinformatics 2009 10:77 doi:10.1186/1471-2105-10-77