problem with ndvi

Hello list,
I am working with landsat images and would like to create a phenological 
cycle with NDVI.
I am using R for that but NDVI values changes if i use on sensor 
reflectance instead of DN values i.e. giving different result in every case.
I tried to compare histograms seems to have changed and I am not getting 
negative values where there is no vegetation but if i use DN values it 
gives negative values to such locations. Do anybody have any idea what 
went wrong??

Thanks in advance and would be much appreciated.

Vikram