Hydraulic Brake Loud Noise and Vibration
As suggested in the comments, follow the burn in procedure. If that fails, then you can try to reset the caliper alignment (follow the installation instructions or one of the many sites on the internet). Also clean the disc with a volatile oil solvent such as alcohol or methylated spirits. 

If that fails, it may be your pads - what did you have and what did you replace them with? Organics tend to make less noise but don't perform as well or last as long, metallic compounds tend to be better performing material and last longer but are more prone to noise.