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The Two Curves Yield anAdjustment Curve
Quantile Normalization• Normalize so that the quantiles of each chipare equal. Simple and fast algorithm. Goal isto give same distribution to each chip.• We will illustrate the algorithm with anexample.
Page 2 and 3:
Outline• What is Low-Level Analys
Page 4 and 5:
High-Level Analysis• Clustering/C
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Brief TechnologyOverview• High de
Page 8 and 9:
Two Probe TypesPM: the Perfect Matc
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Focusing on a SingleGeneChip Cell L
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Hybridization to the Chip
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Chip dat file - checkered board - o
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Chip dat file - checkered board - c
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Constructing a geneexpression measu
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Background/SignalAdjustment• A me
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Normalization“Non-biological fact
Page 24 and 25:
Summarization• Reduce the 11-20 p
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Affymetrix Spike-in Data• 59 chip
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Assessing Bias:Observed Expression
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Assessing Variability:M vs A plots
Page 38 and 39:
Summary of Trade-offsBackgroundMeth
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Scaling is Not Sufficient
Page 45 and 46: Little effect on Spike-insMethodAll
Page 47 and 48: Comparing EstablishedExpression Mea
Page 49 and 50: General Probe LevelModelyij= f( X)+
Page 51 and 52: Fitting the PLM• Robust regressio
Page 53 and 54: Fold ChangeFC = X − XlmWhereXl=
Page 55 and 56: “Robust” t-statistict=Xlsnm2s2l
Page 57 and 58: Limma “ebayes” t-statistic• G
Page 59 and 60: Probe Level Model teststatisticstPL
Page 65: What Happens as the Numberof Arrays
Page 71 and 72: ResultsMethod Individual Models Sin
Page 75 and 76: What is going on here?• Examine r
Page 77 and 78: Low Non-Differential
Page 79 and 80: High Non-Differential
Page 81 and 82: GeneLogic Tonsil dataset
Page 83 and 84: ResultsMethod 3 vs 3 4 vs 4 5 vs 50
Page 86 and 87: Ongoing work in this area• Techno
Page 88 and 89: Additional Slides
Page 90 and 91: Original RMA Background• Convolut
Page 92 and 93: A Standard Curve AdjustmentBased on
Page 94 and 95: γRelates to Concentration
Page 98 and 99: Sort columns of of originalmatrixTa
Page 100 and 101: RMA Model• To each probeset (k),
Page 102 and 103: Basic RMA modelLetthenyij= log N B2
Page 104 and 105: SlopeAllMidLowHighValue0.4930.6650.
Page 106 and 107: SlopeAllMidLowHighValue0.5890.7510.
Page 108 and 109: SlopeAllMidLowHighValue0.6950.820.5
Page 110 and 111: Slope: 0.484
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