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Assessing Variability:M vs A plots• Vertical Axis is M a log2 fold-change.• Horizontal Axis is A an average absoluteexpression value.• Ideally non differential genes tight about M=0
Page 2 and 3: Outline• What is Low-Level Analys
Page 4 and 5: High-Level Analysis• Clustering/C
Page 6 and 7: Brief TechnologyOverview• High de
Page 8 and 9: Two Probe TypesPM: the Perfect Matc
Page 10 and 11: Focusing on a SingleGeneChip Cell L
Page 12 and 13: Hybridization to the Chip
Page 14 and 15: Chip dat file - checkered board - o
Page 16 and 17: Chip dat file - checkered board - c
Page 18 and 19: Constructing a geneexpression measu
Page 20 and 21: Background/SignalAdjustment• A me
Page 22 and 23: Normalization“Non-biological fact
Page 24 and 25: Summarization• Reduce the 11-20 p
Page 26 and 27: Affymetrix Spike-in Data• 59 chip
Page 28 and 29: Assessing Bias:Observed Expression
Page 37 and 38: Detecting DifferentialExpression: R
Page 39: Comparing theNormalization Methods
Page 44 and 45: Variability of Non-DifferentialGene
Page 46 and 47: ROC Curves
Page 48 and 49: Probe Level Models forDetection of
Page 50 and 51: We Will Focus on TwoParticular PLM
Page 52 and 53: Variance CovarianceEstimates• Sup
Page 54 and 55: Simple t-statistict=Xlsnm2s2l ml−
Page 56 and 57: Simple Moderated t-Statistict=snl2s
Page 58 and 59: Probe Level Model teststatisticsΣ
Page 60: A First Comparison• 8 chips from
Page 70 and 71: A Larger Comparison• Look at the
Page 72: More Spike-in Datasets• Two GeneL
Page 76 and 77: Affymetrix Spike-ins
Page 78 and 79: Middle Non-Differential
Page 80 and 81:
GeneLogic AML Spike-ins
Page 82 and 83:
How About With More“Real” Data?
Page 84:
What about the treatmenteffect mode
Page 87 and 88:
Acknowledgements• Terry Speed (UC
Page 89 and 90:
Background Signal Methods• Affyme
Page 91 and 92:
Convolution Model• O = S + N- O i
Page 93 and 94:
What About Non Spike-ins?• We don
Page 95 and 96:
Establishing a RelationshipγBetwee
Page 97 and 98:
Quantile Normalization• Normalize
Page 99 and 100:
Why Quantile Normalization?• Quan
Page 101 and 102:
Probe Level Models are• RMA metho
Page 103 and 104:
Advantages/Disadvantages of RMA/Med
Page 105 and 106:
SlopeAllMidLowHighValue0.630.7840.3
Page 107 and 108:
SlopeAllMidLowHighValue0.690.820.52
Page 109 and 110:
SlopeAllMidLowHighValue0.8561.0410.
Page 111 and 112:
Slope: 0.624
Page 113 and 114:
Slope: 0.683
Page 115:
Slope: 0.847
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