Hi Sam, Did you ever figure out how to get around this issue? I am having the exact same issue when I am running pa.calls on my Expression set. I am also running R version 2.11.1 myself. Fong

Hi Fong, I have pinpointed the problem to the approxfun-function in the stats package (so the base-contribution of the R-software). So I have posted the exact problem onto R-help mailing list and got back some possible explanation: seems to be a small issue with rounding numbers in approxfun-function in the stats-package (that is called within the pa.calls-function) This has nothing to do with the panp-package but might be a small bug in a base-level function: See also: http://r.789695.n4.nabble.com/approxfun-problems-yleft-and-yright- ignored-td2338313.html#a2338313 I'll double check and file a bug report, so it should be fixed in coming R-releases. That said, the bug only seems to show up when a particular data structure is present (where you have two very very similar numbers in negative probeset signals and expression set); I have tried out some commonly used data and there, everything went fine. So the pa.calls function should work fine by default and you would only very rarely run into the problem. I'll keep you posted... Best, Sam On 25 August 2010 22:08, Fong Chun Chan <fongchun at="" interchange.ubc.ca=""> wrote: > Hi Sam, > > Did you ever figure out how to get around this issue? ?I am having the exact > same issue when I am running pa.calls on my Expression set. ?I am also running R > version 2.11.1 myself. > > Fong > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie