"Aiguo Li" <[EMAIL PROTECTED]> wrote in message ...
> Probe id Treat1 Treat2
> AffX-BioB-5_at (2p +M)/4 =2 (2*3+0)/3=2
> FFX-BioB-M_at (2*3+0)/4 =1.7 (2*3+0)/3=2
> AFFX-BioB-3_at (2*2+0)/4 =1 (2*2+0)/3=1.3
> AFFX-BioC-5_at (2*2+1)/4 =1.25 (2*1+1)/3=1
> AFFX-BioC-3_at (2*1+1)/4 = 0.75 (2*2+1)/3=1.7
>
> The denominator is always the # of replicates in each treatment.
Excellent. This is *much* clearer. The following appears to do what you
want. See comments about your code below.
---------------
#!/usr/bin/perl
use warnings;
use strict;
while (<DATA>) {
next unless /^A/;
my @data = split;
print join("\t", $data[0], PA(@data[1..4]), PA(@data[5..7])), "\n";
}
sub PA {
my @treat = @_;
my $m = count('M', @treat);
my $p = count('P', @treat);
return (2*$p + $m) / @treat;
}
sub count {
my $search = shift;
return scalar grep { $_ eq $search } @_;
}
__DATA__
Replicates 1 1 1 1 2 2 2
AFFX-BioB-5_at P P P P P P P
AFFX-BioB-M_at P P P P P P P
[snip]
---------------
> #!usr/bin/perl -w
>
> use strict;
> use warnings;
You don't need both -w and use warnings. I read that "use warnings;" is
slightly preferred.
> my @split;
> my @replicate = ( 5, 3);
> my @ratio;
> my $p=0;
> my $m=0;
> my $a=0;
> my $rep=0;
> my $item;
> my $ratio;
There are way too many variables here. As a general rule you want to declare
the variable right before it's used. You want it in the smallest scope
possible so that you avoid having orphaned variables (you declared it but
forgot to use it). Do not declare $a; it has special meaning. See
"perldoc -f sort".
> open (FILE, "<C:/replicate.txt") or die "Can't open file: $!";
>
>
> while( <FILE> )
> {
> #print;
> chomp;
> @split = split (/\t/, $_);
You are splitting on \t. The data I received were delimited by spaces.
> push (@split, $_);
First you split and store the results in @split. You then add the entire
record to @split also. Is this really necessary?
> #print "$_ \n";
> foreach $rep (@replicate)
@replicate contains 5 and 3. If your code worked, shouldn't it contained 3
and 4? Doesn't this denote "the # of replicates in each treatment."
> {
> for(my $i=1; $i<=$rep; $i++)
> {
> push (@split, $_);
> SWITCH:
> if ($_ =~ "P") {$p++; last SWITCH;}
> if ($_ =~ "M") {$m++; last SWITCH;}
> if ($_ =~ "A") {$a++; last SWITCH;}
Shouldn't this be next instead of last?
> }
> print $p, $m, $a;
> @ratio = (($p*2)+$m)/$rep;
You print these values but never print the result of the equation. You are
also setting an array equal to the result of the equation. You should print
the results of the equation or store it in a *scalar* not an array.
>
>
> }
> }
>
> close FILE;
I would not solve this problem as you attempted here. Please see above.
Good luck,
ZO
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