[Bioperl-l] SiteMatrix changes

[skirov]

>===== Original Message From Hilmar Lapp <hlapp at gmx.net> =====
>On Aug 31, 2006, at 1:26 PM, skirov wrote:
>
>>> If you're going to do the correction, you always do it, not just when
>>> one of the positions contains 0. I imagine you were detecting 0 as an
>>> indicator that no correction had been done, but its possible no
>>> correction has been done even if none of the positions has a 0.
>>
>> Well, if none of the positions is 0, no correction is really
>> necessary.
>
>That's wrong. Refer to my previous email as to why.
>
OK, let me restate that- no correction, sufficiently  simple to be part of 
this package is really aplicable.

>As a trivial example, assume we have 3 events A, B, and C. I sample 5
>times and observe:
>
>    A  B  C
>N  2  2  1
>
>According to this table, the frequency estimate for C would be 0.2,
>and 0.4 for the other two. The true frequencies may, however, be f(A)
>= 0.5, f(B) = 0.48, and f(C) = 0.02.
>
>If I sample 100 times, I might get
>
>     A   B  C
>N  51  47  3
>
>By applying a uniform prior in the form of pseudo-counts to the first
>table, I get:
>
>    A  B  C
>N  3  3  2
>
>with fhat(C) = 0.25 and 0.375 for the other two and it becomes clear
>that I don't have enough data yet.
>
>Applying the pseudo-count prior to the second table yields
>
>    A  B  C
>N 52 48  4
>
>with fhat(C) = 0.04 compared to 0.03 without the pseudo-count
>correction.
>
>You don't apply a prior distribution *after* you have seen the data.
>
>	-hilmar
>
>--
>===========================================================
>: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>===========================================================
>
>
>
>
>
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