Analysis of microarray data - VSN International

18Analysis of Microarray Data in GenStatExplore densityThe Density menu allows you to look at the distributionof the measurements as either a kernel smoothedprobability density or as a cumulative density function.The first is similar to the Histogram display, but the slidescan be plotted on the same graph for easier comparisonsbetween slides. For example, using that data from theHistogram example above, and plotting the variateB1_Mean (the mean background levels of red) withDensity menu, and completing it as shown to the right, and with optionsset as right, gives the following plots.The first graph gives the probability density function (pdf) of the log 2 transformed red background valuesas estimated by a kernel density function for each slide. This shows similar trends as the Histogram menu,but as the pdf curves can be superimposed on the same graph, the comparisons are easier to make.However, these curves require smoothing of the data, and may miss small-scale features that a histogrammay detect. The second curve is cumulative density function (cdf), again estimated from a kernel densityestimator, and allows estimates of the quantiles of the distributions, so for example the median values ofthe logged values can be read off by obtaining the points on the curves where the cumulative percentage is50.Explore 2d plotsThe Density menu allows you to look at the relationshipbetween 2 measurements for each slide. Common plots usedfor microarray are the M-A plot that plots the log of ratio ofred to green against the combined intensity of the twocolours. These two statistics can be calculated using theCalculate | Log-ratios menu covered in the next section. Forexample, using that data from the Histogram example above,and plotting the variate F1_Mean against F2_Mean on thelog 2 scale (the mean foreground levels of red and greenrespectively) with 2D Plots menu, and completing it as shown to the right, and with options set as on thenext page, gives the following plot. Note, Block indexes the print tips that printed the slide, and so on eachslide, the different print tips will be plotted in separate colours, allowing us to look for print tip effects.