Analysis of microarray data - VSN International

14Analysis of Microarray Data in GenStat5. In design 1, any two independent allocations (say A-B and C-D) will give an optimal design. Thetwo comparisons represented on the extra slides will have a higher precision that the rest. In design3, the extra slides A 1 B 1 – A 2 B 1 , and A 1 B 2 - A 2 B 2 give the best standard error for the interaction of0.535.6. The only possible connected design is a loop through all the animals, alternating between the twotreatments. The individual animals are not compared very precisely, with the SED matrix shownbelow. The contrast matrix of (-0.25, -0.25, -0.25, -0.25, 0.25, 0.25, 0.25, 0.25) for the mean of B –A has a standard error or 0.354. Adding 4 extra slides allows more accurate comparisons ofindividuals, and the 4 slides shown below reduce the between animals comparisonsaverage SED from 1.210 to 0.838 (and the maximum from 1.414 to 0.913). The Red Greentreatment standard error is reduced to 0.289, an 18% reduction.A1 B1B1 A2Target A1 A2 A3 A4 B1 B2 B3 B4A1 *A2 1.225 *A3 1.414 1.225 *A4 1.225 1.414 1.225 *B1 0.935 0.935 1.369 1.369 *B2 1.369 0.935 0.935 1.369 1.225 *B3 1.369 1.369 0.935 0.935 1.414 1.225 *B4 0.935 1.369 1.369 0.935 1.225 1.414 1.225 *A2B2A3B3A4B4B2A3B3A4B4A1Added SlidesA1 B2B3 A2A3 B4B1 A4Automatic generation of designsThe Stats | Microarrays | Design | Generate TwoChannel design menu allows you to automaticallygenerate reference, loop and balanced incompleteblock designs. You just need to specify the type ofdesign, the number of treatments, and either the loopincrement (1 always works), or the reference level.With a loop design, you can specify more than oneloop increment to get two complementary loops.Using the Treatments in columns by colour optionputs the design in a format appropriate for pastinginto the Stats | Microarrays | Design | Generate TwoChannel design menu. The spreadsheet to the rightshows the resulting balanced incomplete block design with 4 treatments.For single channel designs, the Stats | Microarrays | Design | Generate SingleChannel design menu just opens the Generate Standard Design menu, as thereare no complications with these designs, as each slide is an independent unit,as in any standard experimental design.