Differentially spliced genes between two samples - how to use FIRMA to do this?

Question

[Enigma]

Hi

I am planning to do FIRMA alternate splicing analysis on a micro array gene expression data to compare the alternate splicing between different tissues and fine a set of genes more alternately spliced in one tissue versus another

Reading the paper, it is not obvious how to find differentially spliced genes between two samples. Anyone has ideas on how to do this?

Answer 1

[Charles Warden]

I don't think there is a gold standard for microarray splicing analysis.

If you have exon-level summarizations, you could try doing some simple statistical analysis. If the change only occurs in a single exon, then maybe something interesting is happening with that exon. However, I don't recall how many probes Affy has per exon (I've typically used the HuGene arrays for gene-level summarization).

You could download a demo version of Partek to see what they have. It looks like they should offer this functionality:

http://www.partek.com/Tutorials/microarray/Exon/Colon_Cancer/Colon_Cancer_ExonAnalysis_tutorial-Exon.pdf

However, I can't really attest to quality of either algorithm.