Making notes in PDF using iBooks

So I just got an iPad, it's a beautiful thing. I wanted to make some notes on a PDF I downloaded from my Uni but am unable to highlight or select words or passages. It's not a scanned document or anything. Any reason why I am unable to do this?
Cheers

As far as I am aware you can only make notes or add highlights to books, and not to PDFs. The GoodReader allows you to make notes and highlight sections of PDFs

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