Here's (the beginning of) your problem:

foreach my $probeset_id (sort keys %{$row{$origin{$pip}}}){
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In the above, you're saying "return the value for key $pip from hash %origin; use that value as a key in hash %row" and so on. Notice the "%origin" in this description? You don't have one. Instead, you have a scalar called $origin - and what you actually mean is

foreach my $probeset_id (sort keys %{$row{$origin}{$pip}}){
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...and so on. The other error you have - a minor one, in comparison to the above - is that you've dug down one level too deep in your last 'foreach' statement:

foreach my $probeseq ( sort keys %{$row{$origin}{$pip}{$probeset_id}{$
+affyscore}{$gc}}){
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If you look back to where you construct that hash, you'll notice that $row{$origin}{$pip}{$probeset_id}{$affyscore}{$gc}} is actually a scalar - not a hash. Trying to extract keys from it, as you do in the above statement, is not likely to be productive. Simply print the value of this variable.

Last of all - this isn't a mistake, but it is likely to lead to one (a mistype):

    @data=split (/\t/,$_);
    my $probeset_id  =  $data[0];
    my $origin       =  $data[1];
    my $probeseq     =  $data[2];
    my $pip          =  $data[3];
    my $gc           =  $data[4];
    my $affyscore    =  $data[5];
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This is unnecessary. Better to use a hash slice:

my ($probeset_id, $origin, $probeseq, $pip, $gc, $affyscore) = split /
+\t/;
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-- 
Human history becomes more and more a race between education and catastrophe. -- HG Wells