GG H1 and JETTA

GG H1: Glue Grant H1
A new human transcriptome array for clinical research designed by Stanford University and Affymetrix.

"This array enables comprehensive examination of multiple mechanisms human cells use to regulate transcriptome in response to diseases including improved analysis of gene expression with completely updated gene annotations and carefully redesigned probes, genome-wide quantitation of gene isoforms and identification of alternative splicing, coding and UTR SNP detection and allele specific expression analysis, examination of non-coding transcription and antisense expression, and the analyses of small RNAs.
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Two significant features:
Software for gene and alternative splicing analysis (JETTA) and visualization
Using exon and junction probes in alternative splicing and isoform analysis
Study of unannotated transcribed units

JETTA is improved and integrative software of some algorithms developed by Wong group for exon array. But it should have more function to deal with non-exon probes, for example junction probes etc. I expect a version of JETTA for Linux in the future.

Anyway, I should admit that GG H1 is a powerful tool to investigate the transcriptome systematically. I just wonder if the hybridization for all of the probes on different regions is uniform. I think the SNPs are detected in DNA level, while splicing and miRNA in the RNA level. How can GG H1 identify all these genotypes in a single array? Anyway,comparing with tilling array, what is the advantage of GG H1? Is it worthy to develop an entirely new product with the existence of exon array and tilling array?

Reference:
http://gluegrant1.stanford.edu/~junhee/JETTA/instructions.html