Analysis of microarray data - VSN International

Analysis of Microarray Data in GenStat 17Exploration of microarray dataThe Explore submenu of the Microarray menu allows various customized plots of microarray data. The 4explore menus are Histograms, Density, 2D Plots and Spatial Plot. These are standard GenStat graphicstypes, which may be found under the Graphics menus, but the microarray menus are customized to allowseparate graphs for each slide, with subsets of slides to be displayed being able to set, as well as doing themanipulation data into the format required for the graphs.Explore histogramThe Histogram menu allows you to look at thedistribution of the measurements from several slides inthe experiment to look for odd slides that have adifferential response to the other slides. For example, ifwe open the file “Data13-6-9.gwb” that was saved fromthe 4 GenePix files opened in the previous example,then we can plot the histograms of variousmeasurements for each slide. To look at the quality andlevel of the slide backgrounds, we could plot thevariates B1_Mean and B2_Mean, which are the meanlevels of red and green respectively around each spot.Completing the Histogram menu as shown to the right,gives the following plots.From these it can be seen that the background levels on slide 13-6 cover a narrower range than the otherslides, and that there is a higher background level on slide 13-7, with a long tail of very high backgroundsaround some spots. Slide 13-9 has lower levels of background than the other slides, but a broaderdistribution. The red backgrounds tend to be lower than the green ones. The menu allows a log 2 transformgiving a histogram of the logged values.