Normalization comparison for a boutique array. MA-plots for four examples of a boutique array designed to profile 109 genes during the late stages of B-lymphocyte differentiation. Each cDNA clone is spotted on the array four times (black points). The MSP titration series are shown as blue points. The black line is the lowess fit through the gene probes only. The red line is the weighted lowess fit with MSP probes up-weighted as described in the methods. The yellow and orange points and lines correspond to the differential expression levels of two house keeping genes, HPRT and GAPDH, respectively. (a, b, d) show examples where the gene probe lowess and the wlowess curves are considerably different from each other. (b, c, d) show examples where house keeping genes give very different intensities from each other and from the wlowess curve.