Figure 1

Plot showing (A) typical poor-quality Affymetrix probe set and (B) the revised probe set used in this study.* OY axis corresponds to probe-dependent signal component, also known as affinity profile. Signals are normalized by RMA method. Black dots = ER–, red dots = ER+. * The set of 11 probes shown in Figure 1A contains seven probes that either do not match the genome and transcriptome (probes 1 to 4) or that are not sufficiently specific for their target sequence and may, therefore, detect multiple genes (probes 6 to 8). Concentrating on an unambiguous part of the probe set (Figure 1B) significantly improves the power of the statistical tests used (eg, a t-statistic of 3.07 comparing expression in estrogen receptor-negative versus expression in estrogen receptor-positive tumors as opposed to a t-statistic of 0.98 when the original Affymetrix probe set is used).