Home - Presentation - ASworkshop

Statistical Issues in the Design and Analysis of Microarray Experiment

Place: Academia Sinica, Taiwan

Date: November 26, 2003

Abstract:

PART  I

Microarray experiments performed in many areas of biological sciences generate large and complex multivariate datasets. This talk addresses statistical design and analysis issues, which are essential to improve the efficiency and reliability of microarray experiments. I will discuss various considerations unique to the design of two-colors spotted microarrays, and examine how different types of replication affect design decisions. We calculate variances of two classes of estimates of differential gene expression based on log ratios of fluorescence intensities from spotted microarray experiments: direct estimates, using measurements from the same slide, and indirect estimates, using measurements from different slides. These variances are compared and numerical estimates are obtained from a small experiment. Some qualitative and quantitative conclusions are drawn which have potential relevance to the design of two-colors microarray experiments.

PART  II

Proper statistical design and analysis is essential to improve the efficiency and reliability of microarray experiments, from the early design and pre-processing stages to higher level analysis. In the first part of the talk, I will illustrate issues relating to design and pre-processing with a study aimed at detecting differential gene expression between selected spliceosome mutants. This data was generated from splice-specific microarrays and featured an unbalanced, nested design with minimal degree of replication. In addition, the design of these arrays provide a platform for comparing the performance of different normalization methods. In the second part of the talk, I will present a microarray experiment that aims to identify spatially differentially expressed genes within the mouse olfactory bulb. Using this data, I will illustrate some of the main steps in the analysis of gene expression data.

Slides: Download [Part I pdf]  [Part II pdf] 

References: 

bulletBook: "Statistical Analysis of Gene Expression Microarray Data", T. P Speed (ed), Chapman & Hall. 
bulletThe following site http://www.statsci.org/micrarra/refs.html maintain by Gordon Smyth provide a good summary of technical reports and published papers on statistical analysis of microarray experiments.