burcu; The <b>Peak Detector.vi</b> has and input that allows you to select between peaks and valleys. Make sure you select "peaks".
However, anyway if you are reading peaks or valleys, you should not be getting negative values. Make sure you are calculating the difference in time between peaks rather than the difference between peak values. It is not strange to get those confused ;) Regards; Enrique Vargas www.visecurity.com