Question: Expression values from Exon Array using affymetrix aroma
3
gravatar for ncl.lazzarini
3.0 years ago by
United Kingdom
ncl.lazzarini90 wrote:

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

aroma exon affymetrix expression R • 1.4k views
ADD COMMENTlink modified 3.0 years ago by raunakms940 • written 3.0 years ago by ncl.lazzarini90
3
gravatar for Neilfws
3.0 years ago by
Neilfws47k
Sydney, Australia
Neilfws47k wrote:

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.

ADD COMMENTlink written 3.0 years ago by Neilfws47k

 

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?

ADD REPLYlink written 3.0 years ago by ncl.lazzarini90

The RMA is the normalization.

ADD REPLYlink written 3.0 years ago by Neilfws47k
0
gravatar for Henrik Bengtsson
3.0 years ago by
United States
Henrik Bengtsson60 wrote:

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.

 

 

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Henrik Bengtsson60
0
gravatar for raunakms
3.0 years ago by
raunakms940
Vancouver, BC, Canada
raunakms940 wrote:

If you want RMA based normalization the turorial is here http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis

ADD COMMENTlink written 3.0 years ago by raunakms940
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