[Bioperl-l] how to use bioperl to do Z-scores test

[Frank Lee]

Thanks very much.  I will try the R-project.


On 6/7/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 
> On Jun 7, 2005, at 12:25 AM, Frank Lee wrote:
> 
> > Hi, Sean
> >
> > What I am doing now is like this:
> >
> > I got a number from my data.  Say 122.     Then I generate one
> > thansand numbers randomly according to similar criteria, Say, (7, 19,
> > 45,199,......................).    I wish to tell whether the result
> > 122  is random distributed in the random dataset or it is small or
> > large.    And I wish to caculate the p-vlaue as a cutoff since I have
> > thousands of such data(set).
> >
> > Can you give me some suggestions?  Thanks!
> >
> 
> You could try using code like:
> 
> #!/usr/bin/perl
> use strict;
> use warnings;
> 
> # Observed data
> my $datapoint=90;
> # generate 1000 random numbers (from 1 to 100)
> my @j;
> for my $i ((1..1000)) {
>    $j[$i-1] = int(rand(100));
> }
> 
> # these lines return the number of permutation values > (<=) the
> observed
> # value.
> my $count_greater = grep {$_>$datapoint} @j;
> my $count_less = grep {$_<=$datapoint} @j;
> 
> # output the result
> # You're mileage may vary depending on if you want a one-sided test or
> two-sided
> print "Original Data Point:  $datapoint\n";
> print "Permutation values greater than Data Point:  $count_greater
> (p=".($count_greater/1000).") \n";
> print "Permutation values less than Data Point:  $count_less
> (p=".($count_less/1000).") \n";
> 
> 
> If you are working with a large dataset, you may really want to
> consider moving over to a statistical package like R, which has many
> facilities for doing all kinds of testing like this (and more).
> 
> Sean
> 
> 
> 
> 
> > On 6/7/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> >> Frank,
> >>
> >> I don't think there is a bioperl module to do a t-test, but I could be
> >> wrong.  But you might want to look here:
> >>
> >> http://search.cpan.org/~yunfang/Statistics-TTest-1.1.0/TTest.pm
> >>
> >> Also, the open-source statistical package R
> >> (http://www.r-project.org) is
> >> quite good for such things and can be scripted or used from perl.
> >> What are
> >> you trying to do?
> >>
> >> Sean
> >>
> >> ----- Original Message -----
> >> From: "Frank Lee" <lifei03 at gmail.com>
> >> To: <Bioperl-l at portal.open-bio.org>
> >> Sent: Monday, June 06, 2005 8:43 PM
> >> Subject: [Bioperl-l] how to use bioperl to do Z-scores test
> >>
> >>
> >>> Can anybody give me some ideas about how to use bioperl module to do
> >>> Z-scores test (Say, Wilcoxon).?
> >>>
> >>> Thanks very much
> >>>
> >>> --
> >>> Do not guess who  I am.  I am not Bush in BlackHouse
> >>>
> >>> _______________________________________________
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> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>
> >>
> >>
> >
> >
> > --
> > Do not guess who  I am.  I am not Bush in BlackHouse
> 
> 


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