基因差异表达分析.ppt

Differential Expression Analysis of Microarray Data
Chunsheng Han, .
Division of Bioinformatics
State Key Laboratory of Reproductive Biology Institute of Zoology, CAS
April 20, 2011
Lecture 8
Bioinformatics
Outline
Microarray data: Warming up!
T-test and other tests
SAM: Significance Analysis of Microarrays
Rank Products and a real application
Data, data, data…: the affymetrix system
Scan probe array
image data
.dat file created
Compute cell intensity data from the image data
intensity data
.cel file created
Analyze expression cell intensity data
expression probe analysis data
.chp file created
.DAT File
.CEL file
Raw data, not background corrected
.CHP File
Background substraction
IM: Ideal MM
3. Tukey biweight
1. Simple average
2.
Performance on corrupted data…
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Discrimination score R
R = (PM - MM) / (PM + MM)
If PM >> MM, then R ≈ 1
If PM = MM, then R = 0
Detection Call Significance
One-Sided Wilcoxon’s Signed Rank Test
p value