conflict with magento

Hi.

I am trying to add an animation to a magento site. I have narrowed the issue down to a conflict with a file called prototype.js but this is an essential file for the site.

In chrome in the console I am getting the messages:

1. Uncaught TypeError: Object [object Object] has no method 'dispatchEvent' prototype.js:4079
2. Uncaught TypeError: Cannot read property 'length' of undefined edge.1.0.0.min.js:206

I hve implemnted the "jQuery.noConflict();"  trick but still no joy.

Any help would be greatly appreciated.

Thanks

Sam