[Bioperl-l] p-value, e-value

[Hilmar Lapp]

Jason Stajich wrote:
> 
> I'm implementing the Bio::Search::HSP::GenericHSP and
> Bio::Search::Hit::GenericHit objects, wanted to clarify our use of e-value
> and p-value.  I think we have been interchanging them and considering p
> and alias of evalue.  

Not really, and it shouldn't be. It's only that BLAST at some
point stopped reporting the p-value, and reported the e-value
instead.

The question is rather what significance() should be. I named it
to have somewhat an abstraction from what in a particular hit
and/or alignment tells you the significance. It could even be a
score sitting behind it. I.e., significance() is (was meant to be)
the general-purpose figure of significance, which an individual
implementation (inheriting class) can map to whatever is
appropriate.

	-hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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