Table 3 Number of differentially expressed genes for the METH experiment. Counts of candidate differentially expressed genes for the METH experiment obtained after (1) removing arrays with high background levels from the analysis or (2) keeping these arrays in the analysis, but down-weighting their expression values using the array quality weights from Figure 4 (b) are given for each comparison of interest. The false discovery rate was controlled to be less than 0.05 in each case. More candidate genes are discovered using array weights.