Comparison of gene expression with histological measurements. Publicly-available breast cancer data sets with histological annotation were used to compare probe set accuracy. a) ESR1 expression levels were estimated using each of the nine manufacturer-defined probe sets (Table 1), or by custom probe sets defined by BrainArray or GATExplorer. For each probe set, a pair of box plots indicates the distribution of expression levels in 77 ER-negative tumors (white) and in 209 ER-positive tumors (red) by protein quantification. b) In a separate data set, ERBB2 expression levels were estimated similarly, and compared in 99 HER2-negative (white) tumors and 33 HER2-positive (red) breast tumors.