Expression values from Exon Array using affymetrix aroma

Question

[ncl.lazzarini]

I downloaded CEL files from Gene Omnibus. I usually get the gene expression values using the R affy library and the function expresso. Unfortunately those CEL files are associated to the Exon Array that can't be processed by expresso. After a research on google I found the aroma package. Apparently this should help me to get what I need, but I couldn't find a simple tutorial that illustrate step by step how to convert CEL files to expression values. Can somebody point me a simple (I'm quite new about R) tutorial/example?

Thanks

Answer 1

[Neilfws]

The recommended Bioconductor package for exon arrays is oligo. Unfortunately the documentation is not great. There's a very basic tutorial here and probably others around the Web.

Stick with Bioconductor; aroma is more trouble than it's worth in my experience.

[ncl.lazzarini]

Thanks for the tutorial. It seems to work. With expresso the valued I obtained could have been used directly for analysis. In that tutorial it says values have to be normalized. Can you tell me how? Is not the RMA enough?

[Neilfws]

The RMA is the normalization.

Answer 2

[Henrik Bengtsson]

The FIRMA method (E. Purdom, K. Simpson, M. Robinson, J. Conboy, A. Lapuk & T.P. Speed, FIRMA: a method for detection of alternative splicing from exon array data. Bioinformatics, 2008) and the FIRMAGene method (Robinson MD and Speed TP Differential splicing using whole-transcript microarrays, BMC Bioinformatics 2009, 10:156) were/are both implemented in/on top of the aroma.affymetrix package. There are some online examples of running FIRMA in the Aroma Framework at http://aroma-project.org/vignettes/. The advantages of using aroma.affymetrix is that you'll never run of memory - if you do on a modern computer I'll trade a reproducible example for a beer.

Answer 3

[raunakms]

If you want RMA based normalization the tutorial is here