The four-dimensional nature of microarray data used for QTL mapping. Recombinant inbred lines (strains) comprise dimension 1; the replicate arrays for each strain, dimension 2. Multiple probes for each probe set comprise dimension 3, and multiple probe sets (transcripts), dimension 4. Green rectangles represent the multiple probe- and replicate-specific expression values that must be collapsed to a single value for QTL mapping. That mapping correlates expression values with genotypes in dimension 1. Heritability-weighted averaging uses information in dimensions 1 and 2 to collapse dimension 3 by weighted averaging. Dimension 2 is collapsed by unweighted averaging.