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Introduction

This week you'll learn how to analyze expression DNA microarray data from the Affymetrix platform using tools from Bioconductor.


Resources


Reading

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.

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To access an instance variable of an S3 object, just use the $ operator instead of @. Limma uses S3 objects as of Nov 2012.


Assignments

Identifying transcription factor targets by microarray analysis of mutant plants

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