[BioC] At a loss on new project with Affymetrix U133 2.0

Joern Toedling toedling at ebi.ac.uk
Wed Oct 29 14:54:21 CET 2008


you might want to have a look at the following packages:

- affy: for importing the data and preprocessing
- arrayQualityMetrics: for quality assessment of the arrays
- hgu133a2.db: for the annotation of the probe sets on the microarray
- limma, siggenes: for finding differentially expressed genes
- topGO, GOstats: find perform gene set enrichment analysis with GO

This list of packages is not meant to be exhaustive, and other
Bioconductor packages surely will help you with these steps just as
nicely. Since your analysis seems to be pretty much standard, there is
lots of documentation that can help you get started. You can find
relevant chapters in the books
- Bioinformatics and Computational Biology Solutions Using R and
- Bioconductor Case Studies
The vignettes of packages limma, affy, topGO etc. may also be very useful.

Daren Tan wrote:
> I am starting a new project using Affymetrix U133 2.0, and hope to seek suggestions on completing the analysis within 1 to 2 months. The objective is to identify differentially expressed genes, and to perform gene ontology analysis. Now I am at a loss given the diverse packages and algorithms to choose from. 
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Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk

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