Alternative Exon Score

[dicty]

Hi,

What's Alternative Exon Score? Is this fold change of Exon
expression? What's the difference between Minimum alternative exon
score and Individual probe set min alt. exon score? Each probeset
should refer to on exon.

I saw these parameter settings, but feel confused.

Thanks,
Dicty

[Nathan Salomonis]

Hi Dicty,

Where do you see "Individual probe set min alt. exon score"? Only probeset
(aka exon) alternative exon scores are considered in AltAnalyze.

The Alternative Exon Score is effectively the splicing-index value for a
probeset. This is effectively the fold change for a probeset (control versus
experiment) after you normalize for gene expression differences in the two
groups. Sometimes a probeset is refered to as an exon, but all AltAnalyze
analyses are probeset-level and sometimes two probesets can be found in one
exon, although, typically they are in distinct regions of the exon that
allow you to detect alternative 5' or 3' splicing, a bleeding exon region or
alternative polyadenylation.

Make sense?

Some more details on this can be found in our FAQ:
http://code.google.com/p/altanalyze/wiki/ScoringMethod
or in our online documentation:
http://www.altanalyze.org/help.htm#options
http://www.altanalyze.org/help.htm#algorithm_description

Best,
Nathan