Analysis of microarray data - VSN International

The final example in this section examines the F values inthe column FRatio[1] from the file “Hyb-ANOVA.gwb”,which contains the treatment F-ratio for the results fromthe Single Channel ANOVA for the 9 Affymetrix slidesconsidered earlier. These are compared with the expectedvalues from an F distribution with 2 and 6 degrees offreedom. As F-ratios are very skewed, this comparison isbest plotted on a probability scale. The resulting graph isshown to the right, and this shows the same result asfound in the False Discovery Rate menu for the samedata, i.e. many more of the probes shown significantdifferential expression than expected under the nullhypothesis of no differential expression.Analysis of Microarray Data in GenStat 49Display volcano plotThis menu shows jointly the level of differentialexpression and the significance on a single graph. It iscalled a volcano plot as the points typically take up a vshape looking like the ash spewing out of a volcano. Thisis because it is rare to get points with very small levels ofdifferential expression, but a high level of significance,and vice versa. In addition, as the significance is onlypositive, the negative and positive expressions are plottedagainst positive values, generally giving a symmetric plot(unless there is a big difference in the number ofpositively and negatively expressed log-ratios). Openingthe menu gives the window to the right. In this case, wewill look at the CEst[1], the contrast between DM andControl from the file “Estimates13-6-9.gsh”, andCPVal[1], the corresponding probability under a twosidednull hypothesis of no differential expression. Todemonstrate the ability to colour the points on anothervariate, we will use the mean intensity of the spots for aprobe over the slides. To add this variate to the Estimatesspreadsheet, open the full data set “Data13-6-9.gwb” anduse the Spread | Calculate | Summary Stats menu toobtain the means of intensity for each probe. Thecompleted dialog that does this is shown to the right.Clicking OK will create a spreadsheet containing themeans (shown on the next page).