Analysis of microarray data - VSN International

10Analysis of Microarray Data in GenStatFor example, if we enter three replicates for fourtreatments (A, B, C, D) in an incomplete blockdesign, we would complete the dialog as shown tothe left. Notice that with three replicates of eachtreatment, we cannot get dye balance, but eachtreatment is used twice with one dye and once onthe other, making the design as balanced aspossible. If we have a series of contrasts betweenthe four treatments, we fill in the name of a matrixin the Contrasts Name edit box, and the number ofrows in the matrix in the Number of Contrasts editbox. The matrix has a row for each contrast, and acolumn for each treatment. If the matrix does notexist, we can create this by clicking the Contrastsbutton, which creates a matrix with the columnslabelled by the treatment labels used in the design spreadsheet and with the number of rows specified. Ifthe name of the contrast matrix or the number of rows has not been entered, you will be prompted forthese.If the four treatments A-D where actually a 2 x 2 factorial combination of two 2 level treatments, we couldcreate a matrix to estimate the main effects of both treatments and the two-way interactions as follows.Initially, the matrix would havedefault values as shown to right,and then you would complete itto obtain the values as shown tothe far right.Clicking the Run button willgenerate some output in theOutput window and the followingtwo spreadsheets, as the Displayin spreadsheet option was set.The first spreadsheet gives the precision of each pairwise comparison between the four treatments. Theleading diagonal is missing, as you do not want to compare a treatment with itself. The comparisons A-Cand B-D are slightly more accurate that the others, because A and C have the same pattern across Red andGreen (2-1) and B and D having the other pattern (1-2). However, the variation in SEDs is quite small (