Hi list, with the discussion of (gc)rma times, I thought it might be opportune to aske what other people are doing about the speed of loess in bioconductor 1.2. for 54 arrays I get a time of over 4 hours (I stopped the process then). After experimenting with the parameters in the code I have gone back to an older version. So far this has caused no problems. Gordon Smyth has suggested going to limma. What are other people doing? >marrayNorm 1.1.3 (installed with bioconductor 1.2) > > unix.time(experiment1.norm<-maNorm(experiment1, norm="loess")) >Timing stopped at: 15358.18 19.85 20734.47 0.00 0.00 > >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 > -- 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.