Analysis of microarray data - VSN International

42Analysis of Microarray Data in GenStatThe options and results to be saved are set with the Options and Store dialogs shown next.The output contains the estimate of π 0 of 0.3745.The plot of π 0 vs. lambda shows how the estimate of π 0flattens off around lambda = 0.4. The estimate of π 0 istaken at the maximum value of lambda, i.e. at lambda= 0.9. An alternative estimate of π 0 could be obtainedby reducing the largest value of lambda in the menu.Histograms of the p values and the resulting q valuesare also plotted (above right) which show thereduction in significance when we use q values. Theplot of the q-values vs. the p-values also shows thisreduction more clearly. The plots of the number oftests vs. the q-values and the number of expected falsepositives are also provided (see next page), and thesecould be used to select a q-value to give an expected number of false positives. Finally, the false discoveryand rejection rates are plotted (see next page) on both the normal and log scale so that small probabilitiescan be examined in more detail. These can be compared with the same graphs produced by the mixturemodel for estimating false discovery rates in the next section.