Comparison of expression of custom designed species-specific probes (Y axis) against the Commercial Agilent 44k array probes (X axis). The log2 expression of custom species-specific probes (Y axis) was plotted against that of their Agilent counterpart targeting the same gene (mean expression value, n = 3 arrays). The dashed diagonal corresponds to equal expression between the two types of probes. The density distribution of the number of pairs of probes is shown as hexagons with increased color intensity. As shown in Panels A and B, the human custom species-specific probes obtain a lower expression than their Agilent counterpart with mouse RNA and the similar results for mouse probes (4.5 median fold reduction, 95% CI: 4.2, 4.9 for human probes; and 9.4 median fold reduction, 95% CI: 8.8, 10.3 for mouse probes; P < 2.2x10-16 for both; Non-parametric Mann-Whitney U tests). Panels C and D show that these species-specific probes of the H&M array perform as well on average as those Agilent probes when exposed to the intended RNAs. Human-mouse gene cross-hybridization patterns we discovered are provided in Dataset S1 (http://lussierlab.org/publications/HsMm_array).