I got the following error from rma >peter48.raw <- ReadAffy(widget=TRUE) >peter48.raw <- rma(peter48.raw) Background correcting Error in density(x, kernel = "epanechnikov", n = 2^14) : x contains missing values This is for 48 mgu74av2 mouse chips. Any suggestions for pinpointing the problem, I would greatly appreciate. windows 2000, R 1.6.2, Bioconductor development release. Dual Xeon 2.8GHz box with 4Gb RAM. Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099

Which development version of affy? There was a devel version in the recent past that was broken and would give this error. The most current version (1.2.15) works for me, so you might try updating. You can also check to see if there actually are missing values in your AffyBatch. pm(peter48.raw)[is.na(pm(peter48.raw))] However, if there are missing values there must be something broken. Jim James W. MacDonald UMCCC Microarray Core Facility 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Dick Beyer <dbeyer@u.washington.edu> 05/02/03 05:41PM >>> I got the following error from rma >peter48.raw <- ReadAffy(widget=TRUE) >peter48.raw <- rma(peter48.raw) Background correcting Error in density(x, kernel = "epanechnikov", n = 2^14) : x contains missing values This is for 48 mgu74av2 mouse chips. Any suggestions for pinpointing the problem, I would greatly appreciate. windows 2000, R 1.6.2, Bioconductor development release. Dual Xeon 2.8GHz box with 4Gb RAM. Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor