文档介绍：Gene expression data: Questions, answers and statistics
Overview
Questions involving microarray data.
Different experimental designs
Case studies, including
Olfactory epithelium,
Olfactory bulb,
Identification of differentially expressed genes,
Pattern searching.
Questions and answers: a point of view
Biological questions first, then statistical methods (design, analysis) and thinking, leading to tentative answers, together with an assessment of the uncertainty in those answers
Rather than beginning with:
Purely exploratory analyses, or modelling either processes or data
Something of each of the last es into most statistical analyses, but only after focussing on biological questions
Biological question
Differentially expressed genes
Sample class prediction etc.
Testing
Biological verification
and interpretation
Microarray experiment
Estimation
Experimental design
Image analysis
Normalization
Clustering
Discrimination
R, G
16-bit TIFF files
(Rfg, Rbg), (Gfg, Gbg)
Which genes are (relatively) up/down regulated?
Samples: liver tissue from each of two kinds of mice, . KO vs. WT, or mutant vs. WT
T
C
n
For each gene form the t statistic:
average of n trt Ms
sqrt(1/n (SD of n trt Ms)2)
n
Which genes are (relatively) up/down regulated?
Samples : as before, but also pooled control liver tissue
T
C*
n
For each gene form the t statistic:
average of n trt Ms - average of n ctl Ms
sqrt(1/n (SD of n trt Ms)2 + (SD of n ctl Ms)2)
C
C*
n
parisons of interest
Samples: Liver tissue from mice treated by cholesterol modifying drugs.
Question 1: Find genes that respond differently between the treatment and the control.
Question 2: Find genes that respond similarly across two or more treatments relative to control.
T1
C
T2
T3
T4
x 2
x 2
x 2
x 2
Interaction?
Samples: treated cell lines at 4 time points (30 minutes, 1 hour, 4 hours, 24 hours)
Question: Which genes contribute to the enhanced inhibitory effect of OSM when it b