I'm happy to help, but I have copied the r-sig-geo list as the community (and you and I) benefit from using the list.
I'm not very clear on what you mean by 'I loose the negative values'. Also, I don't see the connection between the raster you show and the quantile values computed. If you asked for the 0% quantile you should get the lowest available value - (since all pixels are at or above this value). According to the raster info you show that should be -0.893809, but instead your 0% quantile is shown to be 40.00199 Perhaps you have unwittingly mixed up the rasters you are using.
I write in order to ask if someone could indicate me if there is a way to measure and compare between groups the 3D homogeneity of a distribution of points in 3D. I think to some extension in 3D of usual point pattern analysis.