Two-way hierarchical clustering of real-time quantitative reverse-transcription (qRT)-PCR data. (a) The sample-associated dendrogram groups the 126 breast samples profiled by qRT-PCR into the same classes seen by microarray analysis. Samples are grouped into Luminal (blue), HER2+/ER- (pink), Normal-like (green), and Basal-like (red) subtypes. The expression level for each gene is shown relative to the median expression of that gene across all the samples, with high expression represented by red and low expression represented by green. Genes with median expression are black and missing values are gray. (b) A minimal set of 37 'intrinsic' genes was used to classify tumors into their primary 'intrinsic' subtypes. The 'intrinsic' gene set was supplemented using (c) PgR and EGFR, and (d) proliferation genes. The genes in (c) and (d) were clustered separately in order to determine agreement between the minimal 37 qRT-PCR 'intrinsic' set and the larger 402 microarray 'intrinsic' set (see Additional file 1, Supplemental Figure 1). Overall, 114/123 (93%) primary breast samples were classified the same between microarray and qRT-PCR.