Load an iFrame to Drupal with JavaScript
Your code is missing some important stuff. The original code from the Google page you linked yourself:

_gaq.push(function() {
  var pageTracker = _gat._getTrackerByName();
  var iframe = document.getElementById('myIFrame');
  iframe.src = pageTracker._getLinkerUrl('http://www.my-example-iframecontent.com/');
});


So you would end up with something like the following.

&lt;script type="text/javascript"&gt;_gaq.push(function () {
  document.getElementById('myIFrame').src = _gat._getTrackerByName()._getLinkerUrl('http://www.my-example-iframecontent.com/');
});&lt;/script&gt;
&lt;iframe id="myIFrame" height="500px" width="350"&gt;&lt;/iframe&gt;