foreach my $probeset_id (sort keys %{$row{$origin{$pip}}}){

[download]
this construct will not work (like you intended). There is no hash named %origin like in $origin{$pip}. You constructed a hash whose values are references to anonymous hashes (which have no entry in the symbol table and can only be accessed through their reference). Thats fine, you only need to access it through refernces.

Since you have a hash of hashes (of hashes...) better write it like this 

foreach my $probeset_id (sort keys %{$row{$origin}{$pip}}){

[download]
You can retrieve the values like you assigned them. When assigning the values you made use of "autovivification". That is, you relied on Perl to create all hash entries, you referenced. Without "autovivification" your line 
$row{$origin}{$pip}{$probeset_id}{$affyscore}{$gc} =$probeseq;

[download]
would have been written like this 
$row{$origin} = {}; # set value to an empty hash reference 
$row{$origin}{$pip} = {};
$row{$origin}{$pip}{$probeset_id} = {};
$row{$origin}{$pip}{$probeset_id}{$affyscore} = {};
$row{$origin}{$pip}{$probeset_id}{$affyscore}{$gc} =$probeseq;

[download]

In reply to Re: Complex Data Structure by hexcoder
in thread Complex Data Structure by sesemin

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.