基因差异表达分析

Differential Expression Analysis of Microarray DataChunsheng Han, Ph.D.Division of BioinformaticsState Key Laboratory of Reproductive Biology Institute of Zoology, CASApril 20, 2011Lecture 8BioinformaticsOutline1. Microarray data: Warming up!2. T-test and other tests3. SAM: Significance Analysis of Microarrays4. Rank Products and a real applicationData, data, data: the affymetrix systemScan probe arrayimage data .dat file createdCompute cell intensity data from the image dataintensity data.cel file createdAnalyze expression cell intensity dataexpression probe analysis data.chp file created.DAT File.CEL fileRaw data, not background corrected.CHP FileBackground substractionIM: Ideal MM3. Tukey biweight1. Simple average2.Performance on corrupted dataDiscrimination score RR = (PM - MM) / (PM + MM)If PM MM, then R 1If PM = MM, then R = 0Detection Call SignificanceOne-Sided Wilcoxons Signed Rank Testp valueWhere is the from?RDifferential Expression: The affymetrix reportHow is it calculated?SPVi,j = PVi,j + log2(nfi*sfi)Change CallDecide the baseline array and experiment arrayCalculate PM MM of the two arraysOne-Sided Wilcoxons Signed Rank TestGenerate a change p valueMake a change callOutline1. Microarray data: Warming up!2. T-test and other tests3. SAM: Significance Analysis of Microarrays4. Rank Products and a real applicationPopulation 1 Population 21 2Sample1 Sample2X1 X2 tells us about the populationThe sample mean tells us about The t-distribution Founder WS Gosset (1876 to 1937) Wrote under the pseudonym “Student” Mostly worked in tea (t) time ? Hence known as Students t test. Preferable when the n 2 H0: 1 - 2 = 0 H1: 1 - 2 0H0: 1 = 2 H1: 1 2 H0: 1 2H0: 1 - 2 0 H1: 1 - 2 0H0: 1 - 2 H1: 1 - 2 0OROROR Left TailRight TailTwo Tail H1: 1 2Mean systolic BP in nephritis is significantly higher than of normal person100 110 120 130 1400.05Mean systolic BP in nephritis is significantly different from that of normal person0.025 0.025100 110 120 130 140Statistical AnalysiscontrolgroupmeantreatmentgroupmeanIs there a difference?What does difference mean?mediumvariabilityhighvariabilitylowvariabilityThe mean differenceis the same for allthree casesWhat does difference mean?mediumvariabilityhighvariabilitylowvariabilityWhich one showsthe greatestdifference?What does difference mean? a statistical difference is a function of the difference between means relative to the variability a small difference between means with large variability could be due to chance like a signal-to-noise ratiolowvariabilityWhich one showsthe greatestdifference?So we estimatelowvariabilitysignalnoisedifference between group meansvariability of groups=XT - XCSE(XT - XC)= t-value_ _ _-1.960Area = .025Area =.005