Figure 7

Multiple array moderated t statistic ROC curves. These ROC curves display the ability to identify differentially expressed probes based on the moderated t-statistic. In the spike-in experiment, only the spiked-in probes are present in different quantities in the two channels. This t-statistic takes the variance of the fold changes into account in a way that borrows strength across all genes. This is necessary with a small number of arrays to reduce the possibility that genes having extremely small variances, by chance alone, are identified as significant. Here the three pre-processing methods performed equally well. The inset of this figure is the same graph where the x axis has been truncated and 1-specificity has been replaced by counts. This shows the very minor improvement using loess normalization with or without background subtraction compared to Agilent normalization. Agilent, median with and without background subtraction, black, red and blue lines respectively.