Figure 6

CAT plots showing the overlap of top n selected probe sets. Two types of comparisons are made for each of the a) fold change and b) t-test metrics frequently used for selection of regulated probe sets within a simple experimental design such as the one used here (i.e., 15 normal vs. 15 malignant liver samples). For both fold change and t-test metrics, the consistency of regulation events is based on overlapping selection of top n regulated probe sets. First, multiple test sets of 15 normal and 15 malignant samples are used to assess consistency of regulation using the same summarization algorithm over 20 bootstrap iterations with sample replacement. Second, the same test set of 15 normal and 15 malignant samples are used to assess consistency of regulation using different summarization schemes, namely Classic vs. Full refRMA. For each metric, regulation consistency due to summarization scheme is higher than consistency due to different test sets