Preprocessing and quality
assessment of Affymetrix probe level
Dr. R. Irizarry
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
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.