Hi, R2.1.1 Windows XP absolute beginner I'm having problems using the Kooperberg normalization method. Here's a screenshot of my error, along with some background code: ---------------------------- > targets <- readTargets("Targetdyeswap.txt") > RG <- read.maimages(targets$FileName, source="genepix") Read B115_R480_G430.gpr Read B116_R480_G430.gpr > RG$genes <- readGAL("MOB-1-3.anno.gal") > RG$printer <- getLayout(RG$genes) > RGmodel <- kooperberg("B115_R480_G430.gpr", layout=RG$printer, fg="mean", bg="median") Error in get(x, envir, mode, inherits) : variable "B115_R480_G430.gpr" was not found ------------------------------ Why is my filename now being viewed as a variable? Thanks in advance. Matt --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu

library(limma) ?kooperberg Gives the example code as: genepixFiles <- dir(pattern="*\\.gpr$") read.series(genepixFiles, suffix=NULL, skip=26, sep="\t") layout <- getLayout(get(genepixFiles[1])) RGmodel <- kooperberg(genepixFiles, layout=layout) i.e. you need to use read.series to read in your data. Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of scholz at Ag.arizona.edu Sent: 22 August 2005 17:28 To: bioconductor at stat.math.ethz.ch Subject: [BioC] kooperberg syntax Hi, R2.1.1 Windows XP absolute beginner I'm having problems using the Kooperberg normalization method. Here's a screenshot of my error, along with some background code: ---------------------------- > targets <- readTargets("Targetdyeswap.txt") > RG <- read.maimages(targets$FileName, source="genepix") Read B115_R480_G430.gpr Read B116_R480_G430.gpr > RG$genes <- readGAL("MOB-1-3.anno.gal") > RG$printer <- getLayout(RG$genes) > RGmodel <- kooperberg("B115_R480_G430.gpr", layout=RG$printer, > fg="mean", bg="median") Error in get(x, envir, mode, inherits) : variable "B115_R480_G430.gpr" was not found ------------------------------ Why is my filename now being viewed as a variable? Thanks in advance. Matt --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor