Dear scientists,

I have human HTA 2.0 arrays and was using limma to detect gene-level and exon-level differential expression, and was wondering whether there is any package to make use of the junction probesets (JUC in contrast to PSR) to detect alternative splicing events? For the gene-level and exon-level differential expression, I used only PSR probesets, since JUC probesets target splicing sites and are partially redundant between isoforms.

Thank you very much :)

Sincerely,

Sunny

There is no package that I know of, in Bioconductor, and I sort of doubt there ever will be. Unfortunately for those who might want to use these arrays, the interest in developing methods for analysis of microarray data waned in large part about ten years ago, especially for something as complex as the HTA arrays

You might be able to find a commercial product that is intended to analyze these arrays (or use Affy's TAC software), but I can't imagine a PhD statistician trying to get funding to develop methods for these assays when there are so many more interesting (and fundable) projects that they could propose instead.

Thank you very much James!! I appreciate your response. I had the same concern that no one will be interested in investigating time on this type of arrays since nowadays there are many other more interesting things going on. By all means I highly recommend going for RNAseq for differential gene/isoform expression and alt-splicing detection. Fortunately Affymetrix responded to me that they plan to release TAC 3.0 at the end of this year with the function of paired T-test (the current version 2.0 can only perform unpaired T-test). Hopefully this will happen soon!

Thanks again.

Sunny