Analysis of microarray data - VSN International

30Analysis of Microarray Data in GenStatThe spatial plots of the residuals for each slide (the one forslide 13-6 only shown right) allow you to check for spatialeffects that have not been taken into account. The plot for13-6 looks quite clean, but there is perhaps and area at thebottom around row 20 which has too many bright red spots.The M-A plot for 13-6 shows that there is a variancechanges with intensity. The blue lines give approximate95% confidence curves for the points, and the red line is thesmoothed mean, which runs along at approximately zero asdesired. The standardized M-A plot (below right) hasdivided each log-ratio by the estimated confidence limitsused in plotting the blue lines in the plot below left. Thus95% of the points should lie within +/- 1. If we used thelog-ratios from the first plot (below left), there would be atendency to select points with low intensity as these havethe largest variance, and so will produce extreme values more often. Using standardized values would tendto avoid this problem, although in this case the behaviour of the confidence curve around the lowintensities would be cause for concern.