Recommended Tools For Isoform Expresion From ExonArrays

Question

[Ice P]

I'm new to this field. I working on Exonarray data and want to get isoform expressions from CEL files, for further analysis. Could you suggest some tools, preferably in R or other open source. I have tried mmbgx in R but it is very time consuming. How can I be assure that the expression results are good. Is a comparison with RT-PCR results a good choice?

Answer 1

[dario.garvan]

The FIRMA algorithm was designed for such an analysis. The method has been published in a peer-reviewed journal and software is available to use. I am sure if you wanted to publish your findings, you would have to choose a few genes and do qPCR validation of them.