Figure 6

A comparison of p-values obtained from median ANOVA (1-p) and PLM processing of a chosen pair of HGU-133A test conditions. This chart shows that, based on their unadjusted p-values, median ANOVA (1-p) and probe level modeling (PLM) are in fair agreement for unexpressed genes and genes with a factor of two difference in initial concentrations. The tendency for median ANOVA (1-p) to produce, on average, somewhat smaller p-values for spiked-in genes and somewhat larger p-values for non-expressed genes may be due to inaccuracies in chip construction and/or probe level models. There is an even larger difference in p-values for genes whose concentration changes from 512 to 0 pM than for the RMA comparison, but again that has no impact on whether the genes are declared differentially expressed or not.