Hi List, Please excuse the repost. No one responded to my previous post -- and it seems to me to be quite important. The problem is the new marrayNorm 1.1.3 (installed with bioconductor 1.2) -- which seems to get stuck in an endless loop marrayNorm 1.1.3 (installed with bioconductor 1.2) > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) Timing stopped at: 8874.73 19.65 10289.06 0 0 ie I interrupted the process - but with marrayNorm 1.1.1 reinstalled marrayNorm 1.1.1 > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) [1] 803.99 29.73 843.40 0.00 0.00 is there a known problem with this package? bye rob -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://matilda.vu.edu.au/~dunne Email: Rob.Dunne@csiro.au Java has certainly revolutionized marketing and litigation.

>Hi List, > >Please excuse the repost. No one responded to my >previous post -- and it seems to me to be quite >important. > >The problem is the new marrayNorm 1.1.3 >(installed with bioconductor 1.2) -- which seems to get >stuck in an endless loop It isn't in an endless loop, it's just very slow. The problem is the loess function. If you use family="symmetric" and iterations=4 to get a robust loess curve rather than just least squares, then the function is quite slow with lots of data and you get heaps of warnings associated with memory limits and the use of a k-d tree. If you use surface="direct" to avoid the k-d tree and stop the warnings, then the function is very slow indeed with lots of points. You see the result below when you try to run it on 30,000 data points. Versions of marrayNorm prior to 1.1.3 used least squares for the loess curves - much quicker but not ideal as a normalization tool. I have used some tricks to avoid this sort of speed degradation in the limma package. I believe that Jean is in the process of implementing to same sort of thing in the marrayNorm package. Regards Gordon >marrayNorm 1.1.3 (installed with bioconductor 1.2) > > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) >Timing stopped at: 8874.73 19.65 10289.06 0 0 > >ie I interrupted the process - >but with marrayNorm 1.1.1 reinstalled > > marrayNorm 1.1.1 > > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) >[1] 803.99 29.73 843.40 0.00 0.00 > > > >is there a known problem with this package? > > bye > rob > >-- >Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 >CSIRO Mathematical and Information Sciences +61 2 9325 3100 >Locked Bag 17, North Ryde, New South Wales, Australia, 1670 ><http: matilda.vu.edu.au="" ~dunne="">http://matilda.vu.edu.au/~dunne Email: ><https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">Rob.Dunn e at >csiro.au