#!/usr/bin/perl -w

use strict;

use List::MoreUtils qw/any/;

use List::Util qw/sum/;

use Scalar::Util qw/looks_like_number/;

use Statistics::Lite qw/mean stddev/;

use feature 'say';

our $VERSION = '0.001';

######################

#Microarray Filter and Fold Change Finder

######################

#Open data file and read into array:

say "\nMicroarray Filter and Analysis Tool:";

die ("\nUse: perl microarray.pl <Input datafile.txt>") unless @ARGV == 1;

my @genes;

while (<>) {

chomp;

next if /^probes/; # Header line: ignore

my ($name, @values) = split;

# Die on unexpected non-numeric data

die "File '$ARGV' contains non-numeric data at line $."

if any { !looks_like_number($_) } @values;

# We only care about genes which have at least one sample greater than 300.

next unless any { $_ > 300 } @values;

push @genes, { name => $name, values => \@values };

}

say "\nThere are " . scalar(@genes) . " genes that meet filter criteria.\n";

my %score;

for my $gene (@genes) {

my $data = $gene->{values};

my @control = @$data[ 0 .. 19]; # first 20

my @sample = @$data[20 .. 40]; # next 21

my $fldNum = mean(@control) - mean(@sample);

my $fldDenom = stddev(@control) + stddev(@sample);

my $fldScore = $fldNum / $fldDenom;

$score{$fldScore} = $gene->{name};

say "FLD score: $fldScore";

say "Current cycle: ", scalar keys %score

if keys(%score) % 100 == 0;

}

say "Top Ranking Differentially Expressed Genes:";

my $scoreCounter = 1;

foreach my $key (sort keys %score) {

say "$scoreCounter. $score{$key}";

$scoreCounter++;

}