[BioC] error msg w/ read.marrayRaw() : "targets" matched by multiple actual arguments

[Joern Toedling]

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