Thanks Sean. Somehow I had not seen that documentation before. I will attempt setting the seed values and report back. Ross On Wed, Jan 13, 2010 at 2:00 PM, Sean Davis <seandavi@gmail.com> wrote: > On Wed, Jan 13, 2010 at 1:42 PM, Ross Patterson <rossjp@gmail.com> wrote: > > While performing some copy number analysis on data segmented with the > > DNAcopy package, I have noticed some variations in the output data, and > was > > hoping someone here could help shed some light on that. Specifically, > while > > running the DNAcopy segmentation on the exact same input data multiple > > times, I have noticed that the resultant segment data output sometimes > > contains "extra" segments, caused by the discovery of "extra" > breakpoints. > > In fact, the resultant output data is always different. Digging into the > > source code a little bit, I saw what appeared to be calls to some random > > number generating functions, although not being very familiar with > Fortran > > code I could not tell how or why these numbers were being used, or even > if > > that is the source of segmentation discrepancies. I know that in the > last > > few years there have been some changes to the segmentation algorithm to > > allow it to run in near linear time. Did that require introducing > > non-deterministic behavior? Is there a way to force the segmentation > > algorithm to run deterministically, such that the output data can be > > identically reproduced every time the segmentation is run? > > Hi, Ross. > > DNAcopy uses an empirical distribution for determining significance. > The help for segment() gives some details. The authors can perhaps > comment on whether or not there is a way to make things run > deterministically. > > Sean > -- ross [[alternative HTML version deleted]]