基因差异表达分析

Analyze expression cell intensity data expression probe analysis data .chp file created
.DAT File
.CEL file
Raw data, not background corrected
.CHP File
Outline
1. Microarray data: Warming up! 2. T-test and other tests 3. SAM: Significance Analysis of Microarrays 4. Rank Products and a real application
Is there a difference?
between you…means, who is meaner?
T-test
1.
Test for single mean Whether the sample mean is equal to the predefined population mean ?
H0: 1 - 2 0 H1: 1 - 2 > 0 H0: 1 - 2 H1: 1 - 2 < 0
Two Tail
Right Tail Left Tail
OR
OR
Mean systolic BP in nephritis is significantly higher than of normal person
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
Setting Up the Hypothesis
H0: 1 = 2 H1: 1 2
H0: 1 2 H1: 1 > 2 H0: 1 2 H1: 1 < 2
OR
H0: 1 -2 = 0 H1: 1 - 2 0
Detection Call Significance
p value
One-Sided Wilcoxon’s Signed Rank Test
Where is the from?
R
Differential Expression: The affymetrix report
How is it calculated?
wk.baidu.com
µ tells us about the population Population 1 Population 2
µ1
µ2
Sample1
X1 The sample mean tells us about µ
X2
Sample2
The t-distribution
• • • • • •
Founder WS Gosset (1876 to 1937) Wrote under the pseudonym “Student” Mostly worked in tea (t) time ? Hence known as Student's t test. Preferable when the n < 60 Certainly if n < 30
Background substraction
IM: Ideal MM
Performance on corrupted data…
1. Simple average 2.
3. Tukey biweight
∑ ∑
Discrimination score R
R = (PM - MM) / (PM + MM) If PM >> MM, then R ≈ 1 If PM = MM, then R = 0
2. Test for difference in means Whether the CD4 level of patients taking treatment A is equal to CD4 level of patients taking treatment B ?
3. Test for paired observation Whether the treatment conferred any significant benefit ?
SPVi,j = PVi,j + log2(nfi*sfi)
Change Call
Decide the baseline array and experiment array Calculate PM – MM of the two arrays
One-Sided Wilcoxon’s Signed Rank Test
100
110
120
130
140
Mean systolic BP in nephritis is significantly different from that of normal person
Lecture 8 Bioinformatics
Differential Expression Analysis of Microarray Data
Chunsheng Han, Ph.D. Division of Bioinformatics State Key Laboratory of Reproductive Biology Institute of Zoology, CAS April 20, 2011
Generate a change p value Make a change call
Outline
1. Microarray data: Warming up! 2. T-test and other tests 3. SAM: Significance Analysis of Microarrays 4. Rank Products and a real application