医学统计学（扬州大学）Introduction to analysis of microarray data.pptVIP

Introduction to analysis of microarray data David Edwards The Microarray Study Process Study Objectives Class comparison: differential expression Class prediction: classification Class discovery: clustering The problem How to identify genes whose expression level changes across conditions in the study? Outline The study may have different purposes, eg: Comparison of two groups (eg treatment vs control) Comparison of more than two groups More than one comparison (eg 2 treatments, 3 different timepoints) Additive and multiplicative scales Most statistical models use additive scales and constant variance Gene expression appears to work more on a multiplicate scale (fold changes rather than expression differences), and the variance in gene expression depends on its absolute value. Conclusion: transform the data by taking logarithms (conventionally base 2). Fold Change Log Ratios We have transformed our data by taking logarithms! So differences are log-ratios (log fold changes) log(a/b) = log(a) – log(b) With two-channel (cDNA) data the numbers we analyze (usually) are the within-spot log-ratios: M = log(R) – log(G) To estimate log fold change across replicate slides we compute the average log-ratio across the replicates. With one-channel (affy) data the numbers we analyze are the logs of the expression measures (eg rma) To estimate log fold change between two groups of arrays we compute the average log-expression within each group and calculate the difference. LR = (? Y1i)/n1 – (? Y2i)/n2 Analysis Some examples of methods Two-sample t-test Linear regression yt = y0 + ˉ Z y0 baseline expression (before treatment) Z (0=control, 1=treatment) ˉ group effect ANOVA models Non-parametric tests .... Multiplicity Typically a list of p-values is obtained, one per gene. Now we need to select the ones likely to be differentially expressed. If we used p0.05 as criterion this would lead to 1000 (=0.05x20000) genes being selected even though there was no d