Are the input signals correctly for filter computation?
Good question, you should subtract DC offset. Other things, declare data1 and data2 as signed. And you don't need time measurements anymore, otherwise you are reading input twice.
// int data1 = analogRead(analogPin); <-- int, not unsigned int !
data1 = analogRead(0) -512; //Read Analog channels
data2 = Filter.run(data1); //Read the filtered signal