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

[Sean Davis]

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