This site is organized as follows
This section discusses how many replicates are needed, whether to pool samples, and designs for two color arrays.
Pre-processing of Spotted Arrays
This section discusses steps along the way from quantification of the image, through background correction, quality control, and normalization, to obtain reliable estimates of relative gene abundance in the samples.
Pre-processing of Affymetrix Chips
The Affymetrix multiple-probe system offers a unique set of statistical challenges before one even gets to interpreting biological meaning. This section discusses image quantification and background, MAS5.0, normalization, multi-chip algorithms for estimation, and model-based quality control..
A preliminary examination of data confirms that groups are homogeneous. Many studies aim to find unknown co-regulated genes. This section discusses how to achieve these goals using multi-dimensional scaling, and clustering.
Statistical Tests for Identifying Differentially Expressed Genes
This section discusses methods and problems in determining which genes are differentially expressed between groups of samples, covering t-tests, multiple-testing corrections, false discovery rate, empirical Bayes methods, and analysis of variance.
