Analysis of microarray data - VSN International

62Analysis of Microarray Data in GenStatTo analyse the results across the 16 slides, asmall data set is required which provides thetreatments applied to each slides. To do this anempty spreadsheet with 3 columns and 16rows can be created using the menu shownright. This menu can be opened by selectingNew from the File menu and then selectingthe Spreadsheet tab.The data can easily be entered into the emptyspreadsheet. The spreadsheet below rightshows the data that should be entered, with thethree columns named SlideName, Red_Treat,and Green_Treat. Note that the columnsRed_Treat and Green_Treat have been converted to factors.The factors columns Green_Treat and Red_Treat mustcontain the same set of factor levels or labels. In thisexample, the columns should be created such that they bothhave three labels (KnockOut, Normal and Reference).To analyse the data select the Estimate Two Channel Effectsitem from Analyse on the Microarray menu. The picturebelow shows the resulting menu containing settings to run theanalysis.Results can be saved into data structures simultaneously withthe analysis by clicking the Store button (before clickingRun) and specifying the names of the new structures. Thesestructures can also be displayed into spreadsheets byselecting the Display in Spreadsheet.