PERL Beginners - how to use perl module to do Z-scores test (Say, Wilcoxon)

Author

how to use perl module to do Z-scores test (Say, Wilcoxon)

Frank Lee

2005-06-07, 3:55 am

Can anybody give me some ideas about how to use perl module to do
Z-scores test (Say, Wilcoxon).?

Thanks very much!

--=20
Do not guess who I am. I am not Bush in BlackHouse

Chris Devers

2005-06-07, 3:55 am

On Tue, 7 Jun 2005, Frank Lee wrote:

> Can anybody give me some ideas about how to use perl module to do
> Z-scores test (Say, Wilcoxon).?

1. Find the module.

2. Look up the Perldoc that describes how to use it.

3. Use it.

I'll be glad to help you a bit with step #1 there.

A search for Z-score on search.cpan.org --

<http://search.cpan.org/search?query=z-score&mode=all>

-- turns up a number of hits, all of which seem to be applying the
concept of Z-scores to different problem domains. Depending on what
you're doing, one of these may be helpful to you. To pick one at random,
the Bio::Search::HSP::HMMERHSP module has the following:

Plus Bio::Seach::HSP::GenericHSP methods
[...]
-score => score value for HSP (typically z-score but
depends on analysis)

<http://search.cpan.org/dist/bioperl...HSP/HMMERHSP.pm>

That may or may not be useful to you.

If you need something more generic, maybe a search for "statistics" will
provide a more general-purpose module. Sure enough, this turns up:

Bundle::Math::Statistics
<http://search.cpan.org/~smueller/Bu...1/Statistics.pm>

That, in turn, includes modules like Statistics::Contingency, et al.

<http://search.cpan.org/~kwilliams/S.../Contingency.pm>

Maybe that'll help.

As a search for "Wilcoxon" doesn't seem to turn up any hits, you may be
running out of options. If you're still stuck, the next place to look
may be the book _Mastering Algorithms with Perl_, which has a chapter or
two on statistical programming in Perl. Unfortunately, I don't see
Z-score in the index, but I do see Z-test; my statistics are too rusty
for me to remember if these are the same thing or not.

<http://www.oreilly.com/catalog/maperl/inx.html#Z>

But there's a bunch of samples of statistical algorithms in that book,
along with explantions of how they work & how to use them. If all else
fails, that might be enough to help you get started on rolling your own.

Helpful?

Sorry to only provide pointers rather than direct help, but as I, err,
don't remember much about Z-scores, I can't be more concrete than that.
If none of this has helped, then maybe it would help if you could
describe the basic algorithm & the list readers can help show you how to
implement it in Perl... :-/

--
Chris Devers

Frank Lee

2005-06-07, 3:55 am

Hi, Chris, =20

That's very nice! It is very helpful for me. I can use the Z-test in
the Mastering Algorithms with Perl. Thanks very much!

Frank

On 6/7/05, Chris Devers <cdevers@pobox.com> wrote:
> On Tue, 7 Jun 2005, Frank Lee wrote:
>=20
>=20
> 1. Find the module.
>=20
> 2. Look up the Perldoc that describes how to use it.
>=20
> 3. Use it.
>=20
>=20
> I'll be glad to help you a bit with step #1 there.
>=20
>=20
> A search for Z-score on search.cpan.org --
>=20
> <http://search.cpan.org/search?query...core&mode=3Dall>
>=20
> -- turns up a number of hits, all of which seem to be applying the
> concept of Z-scores to different problem domains. Depending on what
> you're doing, one of these may be helpful to you. To pick one at random,
> the Bio::Search::HSP::HMMERHSP module has the following:
>=20
> Plus Bio::Seach::HSP::GenericHSP methods
> [...]
> -score =3D> score value for HSP (typically z-score but
> depends on analysis)
>=20
> <http://search.cpan.org/dist/bioperl...HSP/HMMERHSP.pm>
>=20
> That may or may not be useful to you.
>=20
> If you need something more generic, maybe a search for "statistics" will
> provide a more general-purpose module. Sure enough, this turns up:
>=20
> Bundle::Math::Statistics
> <http://search.cpan.org/~smueller/Bu...-1.01/Statisti=
cs.pm>
>=20
> That, in turn, includes modules like Statistics::Contingency, et al.
>=20
> <http://search.cpan.org/~kwilliams/S...y-0.06/Conting=
ency.pm>
>=20
> Maybe that'll help.
>=20
> As a search for "Wilcoxon" doesn't seem to turn up any hits, you may be
> running out of options. If you're still stuck, the next place to look
> may be the book _Mastering Algorithms with Perl_, which has a chapter or
> two on statistical programming in Perl. Unfortunately, I don't see
> Z-score in the index, but I do see Z-test; my statistics are too rusty
> for me to remember if these are the same thing or not.
>=20
> <http://www.oreilly.com/catalog/maperl/inx.html#Z>
>=20
> But there's a bunch of samples of statistical algorithms in that book,
> along with explantions of how they work & how to use them. If all else
> fails, that might be enough to help you get started on rolling your own.
>=20
> Helpful?
>=20
> Sorry to only provide pointers rather than direct help, but as I, err,
> don't remember much about Z-scores, I can't be more concrete than that.
> If none of this has helped, then maybe it would help if you could
> describe the basic algorithm & the list readers can help show you how to
> implement it in Perl... :-/
>=20
>=20
>=20
> --
> Chris Devers
>=20

--=20
Do not guess who I am. I am not Bush in BlackHouse

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