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Google Analytics: How to setup ecommerce tracking in Google Analytics if ecommerce platform is setup on subdomain?
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Beach Boy Donnie, SEO Entrepreneur answered:

always save the original profile as a backup.

that said, this is an easy problem to solve. you just need to use this line of code above the "trackpageview" line....
_gaq.push(['_setDomainName', 'example.com']);

here's an easy tool to help http://gaconfig.com/one-domain-with-subdomains/

here's more details for your developer https://developers.google.com/analytics/devguides/collection/gajs/gaTrackingSite

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