Graphical Representations

Although they are not particularly informative in terms of hard data, graphical representations of microarray data are quite useful. The distribution and spread of the array data is often a convenient method to visualize the changes occurring in the two samples studied. For this purpose there are two commonly used scatter-plots. A log R/G plot shows the log transformed intensity of one channel plotted against the other. This is a very straightforward and intuitive plot, but the high correlation between the two channel intensities can make visualizing smaller outliers harder. A better way to view the distribution of microarray data is to use an MA plot where the average spot intensity (A) is plotted along the x axis and the log2 ratio (M) is plotted on the y axis [44]. This makes it easier to see those genes differentially expressed. The MA plot is also used to visualize the relationship between spot intensity and the level of expression before and after normalization procedures like LOWESS to assess their effect and accuracy. The results of clustering are often displayed as a tree, which leads to a colored representation of the intensity over a time course (for example) so that the relationship between genes' expression profiles are easy to see. Array data can be presented in numerous other ways, too, most of which help us to wade through the mass of data generated by the experiment.

0 0

Post a comment