《基因差异表达分析》PPT课件

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1、DifferentialExpressionAnalysisofMicroarrayDataChunshengHan,Ph.D.DivisionofBioinformaticsStateKeyLaboratoryofReproductiveBiologyInstituteofZoology,CASApril20,2011Lecture8BioinformaticsOutlineMicroarraydata:Warmingup!T-testandothertestsSAM:SignificanceAnalysisofMicro

2、arraysRankProductsandarealapplicationData,data,data…:theaffymetrixsystemScanprobearrayimagedata.datfilecreatedComputecellintensitydatafromtheimagedataintensitydata.celfilecreatedAnalyzeexpressioncellintensitydataexpressionprobeanalysisdata.chpfilecreated.DATFile.CE

3、LfileRawdata,notbackgroundcorrected.CHPFileBackgroundsubstractionIM:IdealMM3.Tukeybiweight1.Simpleaverage2.Performanceoncorrupteddata…∑∑DiscriminationscoreRR=(PM-MM)/(PM+MM)IfPM>>MM,thenR≈1IfPM=MM,thenR=0DetectionCallSignificanceOne-SidedWilcoxon’sSignedRankTestpva

4、lueWhereisthefrom?RDifferentialExpression:TheaffymetrixreportHowisitcalculated?SPVi,j=PVi,j+log2(nfi*sfi)ChangeCallDecidethebaselinearrayandexperimentarrayCalculatePM–MMofthetwoarraysOne-SidedWilcoxon’sSignedRankTestGenerateachangepvalueMakeachangecall

5、OutlineMicroarraydata:Warmingup!T-testandothertestsSAM:SignificanceAnalysisofMicroarraysRankProductsandarealapplicationPopulation1Population2µ1µ2Sample1Sample2X1X2µtellsusaboutthepopulationThesamplemeantellsusaboutµThet-distributionFounderWSGosset(1876t

6、o1937)Wroteunderthepseudonym“Student”Mostlyworkedintea(t)time?HenceknownasStudent'sttest.Preferablewhenthen<60Certainlyifn<30Isthereadifference?betweenyou…means,whoismeaner?T-testTestforsinglemeanWhetherthesamplemeanisequaltothepredefinedpopulationmean?2.Testfordif

7、ferenceinmeansWhethertheCD4levelofpatientstakingtreatmentAisequaltoCD4levelofpatientstakingtreatmentB?3.TestforpairedobservationWhetherthetreatmentconferredanysignificantbenefit?SettingUptheHypothesisH0:12H1:1>2H0:1-2=0H1:1-20H0:1=2H1:12

8、H0:12H0:1-20H1:1-2>0H0:1-2H1:1-2<0ORORORLeftTailRightTailTwoTailH1:1<2MeansystolicBPinnephritisissignifica