Hi all, When loading cDNA data using read.marrayRaw(), everything works fine until I specify an marrayInfo object as targets parameter of read.marrayRaw() i.e. files_s <- c("slide_63_trunc.csv", "slide_64_trunc.csv", "slide_65_trunc.csv", "slide_72_trunc.csv") >maraw <- read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = >"Ch1 B Mean", name.Rf = "Ch2 Mean", name.Rb = "Ch2 B Mean", name.W = NULL, >layout = NULL, gnames = NULL, targets = NULL, notes = NULL, sep = ",") Reading ... ./slide_63_trunc.csv Reading ... ./slide_64_trunc.csv Reading ... ./slide_65_trunc.csv Reading ... ./slide_72_trunc.csv Warning message: incomplete final line found by readLines on `./slide_63_trunc.csv' ..specifying a targets file (which i adapted as a test from the swirl data in marray package) : s.targets <- read.marrayInfo(fname = "SSample.txt") s.targets An object of class "marrayInfo" @maLabels [1] "slide_63_trunc.csv" "slide_64_trunc.csv" "slide_65_trunc.csv" "slide_72_trunc.csv" @maInfo Names slide number experiment Cy3 experiment Cy5 date comments 1 slide_63_trunc.csv 63 swirl wild type 9/20/01 NA 2 slide_64_trunc.csv 64 wild type swirl 9/20/01 NA 3 slide_65_trunc.csv 65 swirl wild type 11/8/01 NA 4 slide_72_trunc.csv 72 wild type swirl 11/8/01 NA @maNotes [1] "SSample.txt" now specifying an marrayInfo object with read.marrayRaw() : maraw2 <- read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = "Ch1 B Mean", name.Rf = "Ch2 Mean", name.Rb = "Ch2 B Mean", name.W = NULL, layout = NULL, gnames = NULL, targets = NULL, notes = NULL, sep = ",", targets = s.targets) Error in read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = "Ch1 B Mean", : formal argument "targets" matched by multiple actual arguments Not sure what's happening here. I've got : OS X 10.3.9 R 2.0.1 for Aqua GUI marray 1.5.30 Thanks in advance for any help, Ken

Ken Termiso wrote: >Hi all, > >When loading cDNA data using read.marrayRaw(), everything works fine until I >specify an marrayInfo object as targets parameter of read.marrayRaw() > >i.e. > >files_s <- c("slide_63_trunc.csv", "slide_64_trunc.csv", >"slide_65_trunc.csv", "slide_72_trunc.csv") > > >>maraw <- read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = >>"Ch1 B Mean", name.Rf = "Ch2 Mean", name.Rb = "Ch2 B Mean", name.W = NULL, >>layout = NULL, gnames = NULL, targets = NULL, notes = NULL, sep = ",") >> >> >Reading ... ./slide_63_trunc.csv >Reading ... ./slide_64_trunc.csv >Reading ... ./slide_65_trunc.csv >Reading ... ./slide_72_trunc.csv >Warning message: >incomplete final line found by readLines on `./slide_63_trunc.csv' > > > >..specifying a targets file (which i adapted as a test from the swirl data >in marray package) : > >s.targets <- read.marrayInfo(fname = "SSample.txt") > >s.targets >An object of class "marrayInfo" >@maLabels >[1] "slide_63_trunc.csv" "slide_64_trunc.csv" "slide_65_trunc.csv" >"slide_72_trunc.csv" > >@maInfo > Names slide number experiment Cy3 experiment Cy5 date >comments >1 slide_63_trunc.csv 63 swirl wild type 9/20/01 > NA >2 slide_64_trunc.csv 64 wild type swirl 9/20/01 > NA >3 slide_65_trunc.csv 65 swirl wild type 11/8/01 > NA >4 slide_72_trunc.csv 72 wild type swirl 11/8/01 > NA > >@maNotes >[1] "SSample.txt" > >now specifying an marrayInfo object with read.marrayRaw() : > >maraw2 <- read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = >"Ch1 B Mean", name.Rf = "Ch2 Mean", name.Rb = "Ch2 B Mean", name.W = NULL, >layout = NULL, gnames = NULL, targets = NULL, notes = NULL, sep = ",", >targets = s.targets) >Error in read.marrayRaw(fnames = files_s, name.Gf = "Ch1 Mean", name.Gb = >"Ch1 B Mean", : > formal argument "targets" matched by multiple actual arguments > > > If you look in your function call, you see that indeed you have 'targets=NULL' in the third line and then again 'targets=s.targets' in the fourth line. This double specification generally won't work. Try removing the 'targets =NULL'. Regards, Joern