Preprocessing and quality assessment of Affymetrix probe level data.

Dr. R. Irizarry
Associate Professor
Johns Hopkins

In this session I will describe one of the most popular Bioconductor tools: the packages for preprocessing Affymetrix GeneChip arrays. Specifically we will show how to access and manipulate PM and MM data, explain and implement some of the most popular preprocessing algorithms, and perform some quaility assessment with the affyPLM package.

From Gene List to Final Result; Creating useful output from Microarray

James MacDonald
University of Michigan

Producing a list of differentially expressed genes is only the first half of a microarray analysis. For this list to be truly useful, the genes must be annotated in some way and presented in a clear and usable format.

In this tutorial we will explore various methods available in Bioconductor packages to append useful information to a list of genes and output in various formats (HTML tables, text files, pdf documents). In addition, we will discuss small 'wrapper' functions that can be used to simplify and/or automate the production of these documents. We will focus primarily on Affymetrix data, but many of the techniques are directly applicable to spotted cDNA as well as other oligonucleotide microarray platforms.