This week you'll learn how to analyze expression DNA microarray data from the Affymetrix platform using tools from Bioconductor.
- limma Linear models for microarray data http://www.bioconductor.org/packages/release/bioc/html/limma.html
- affy Methods for Affymetrix Oligonucleotide Arrays http://www.bioconductor.org/packages/release/bioc/html/affy.html
Chapter 8 Single-Channel Experimental Designs from the Limma User's Guide (see attached files for a copy from November 2012). Today's assignment is based on the two-factor experiment analysis described in Chapter 8.
Chapter 9 Object-Oriented Programming from The Art of R Programming by Norman Matloff. Read this to get an overview of S3 and S4 objects. Bioconductor packages use both S3 and S4 objects. To use Bioconductor productively, it's very helpful to understand how to work with both S3 and S4 objects. A rough draft, open access version of the text is available from the author's Web site.