Analysis of microarray data - VSN International

Analysis of Microarray Data in GenStat 1ContentsMicroarray example files ............................................................................................................................... 2Introduction.................................................................................................................................................... 3Microarrays.................................................................................................................................................... 5Design of two-colour microarray experiments .............................................................................................. 71. Reference designs ...................................................................................................................... 72. Loop designs .............................................................................................................................. 83. Balanced incomplete block designs........................................................................................... 8Structured treatments ............................................................................................................................. 8Examples of contrast matrices ............................................................................................................... 9Example using the Microarray Design menu......................................................................................... 9Blocking and randomization in microarray designs ............................................................................ 12Microarray design exercises ................................................................................................................ 12Solutions to design exercises ............................................................................................................... 13Automatic generation of designs ......................................................................................................... 14Reading microarray data.............................................................................................................................. 15Exploration of microarray data .................................................................................................................... 17Explore histogram................................................................................................................................17Explore density .................................................................................................................................... 18Explore 2d plots ................................................................................................................................... 18Explore spatial plots............................................................................................................................. 20Calculations for microarray data.................................................................................................................. 21Calculate log-ratios .............................................................................................................................. 21Background correction..................................................................................................................... 21Calculate Affymetrix expression values .............................................................................................. 23RMA algorithm................................................................................................................................24MAS 4.0 algorithm .......................................................................................................................... 26MAS 5.0 algorithm .......................................................................................................................... 26Normalization of microarray data................................................................................................................ 27One channel (Affymetrix).................................................................................................................... 27Two channel......................................................................................................................................... 29Analysis of microarray data......................................................................................................................... 33Estimate two-channel effects ............................................................................................................... 33One channel ANOVA.......................................................................................................................... 35One Channel Regression Analysis....................................................................................................... 36Robust means analysis ......................................................................................................................... 38Empirical Bayes error estimation......................................................................................................... 39False discovery rate.............................................................................................................................. 40False Discovery Rate using Bonferroni Method.............................................................................. 41Display microarray results ........................................................................................................................... 47Display QQ plot ................................................................................................................................... 47Display volcano plot ............................................................................................................................ 49Cluster microarray probes or targets............................................................................................................ 51Cluster Probes/Genes........................................................................................................................... 51Cluster targets/slides ............................................................................................................................ 53Two-way clustering ............................................................................................................................. 54Two-channel microarray example ............................................................................................................... 55Affymetrix microarray example .................................................................................................................. 65References.................................................................................................................................................... 68