Density plots of probe intensities before and after a filtering step. The density distributions are illustrated for MG1655 probes and non-MG1655 probes separately. Log2 intensity data are from a representative MG1655 control sample. (a) Before filtering, all probes are divided into MG1655 probes (green lines) and non-MG1655 probes (red lines). It is clear that many probes initially designed for groups containing MG1655 genes do not hybridize well to these, resulting in low intensity (green arrow). Conversely, probes initially designed for groups without MG1655 genes cross-hybridize as if present in MG1655 (red arrow). (b) After filtering probes, the remaining probes have the expected hybridization profile.