Principal Component Analysis of preprocessing algorithms in variant A. Plots present Principal Component Analysis of preprocessing algorithms on sample types A and B from MAQC study. Algorithms using the MM probes are marked green while the PM-only algorithms are marked red. (A) PCA of values of Welch's t-statistic from microarray and qRT-PCR detection of differentially expressed genes. (B) PCA of values of fold change between groups. In both cases the new annotation was used. Axes are labelled with percentage of total variability explained by PC1 and PC2. It should be noted that in this technical comparison we used samples of original RNA instead of mixtures C and D.