[BioC] Error with read.maimages

[lapereir at uc.cl]

HI!!

I am sorry, i read the posting guide but for some reason i dont read that
requirement. So here i write the output of sessionInfo(), also include the
traceback() ouput and Sys.getlocale().

> Sys.getlocale()
[1] "en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8"

> traceback()
6: gsub("\\.", "\\\\.", x)
5: protectMetachar(allcnames[i])
4: grep(protectMetachar(allcnames[i]), text.to.search)
3: read.columns(fullname, required.col, text.to.search, skip = skip,
       sep = sep, quote = quote, stringsAsFactors = FALSE, fill = TRUE,
       flush = TRUE, ...)
2: switch(source2, quantarray = {
       firstfield <- scan(fullname, what = "", sep = "\t", flush = TRUE,
           quiet = TRUE, blank.lines.skip = FALSE, multi.line = FALSE,
           allowEscapes = FALSE)
       skip <- grep("Begin Data", firstfield)
       if (length(skip) == 0)
           stop("Cannot find \"Begin Data\" in image output file")
       nspots <- grep("End Data", firstfield) - skip - 2
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, nrows = nspots, flush = TRUE, ...)
   }, arrayvision = {
       skip <- 1
       cn <- scan(fullname, what = "", sep = sep, quote = quote,
           skip = 1, nlines = 1, quiet = TRUE, allowEscape = FALSE)
       fg <- grep(" Dens - ", cn)
       if (length(fg) != 2)
           stop(paste("Cannot find foreground columns in", fullname))
       bg <- grep("^Bkgd$", cn)
       if (length(bg) != 2)
           stop(paste("Cannot find background columns in", fullname))
       columns <- list(R = fg[1], Rb = bg[1], G = fg[2], Gb = bg[2])
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, flush = TRUE, ...)
       fg <- grep(" Dens - ", names(obj))
       bg <- grep("^Bkgd$", names(obj))
       columns <- list(R = fg[1], Rb = bg[1], G = fg[2], Gb = bg[2])
       nspots <- nrow(obj)
   }, bluefuse = {
       skip <- readGenericHeader(fullname, columns = c(columns$G,
           columns$R))$NHeaderRecords
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, flush = TRUE, ...)
       nspots <- nrow(obj)
   }, genepix = {
       h <- readGPRHeader(fullname)
       if (verbose && source == "genepix.custom")
           cat("Custom background:", h$Background, "\n")
       skip <- h$NHeaderRecords
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, flush = TRUE, ...)
       nspots <- nrow(obj)
   }, smd = {
       skip <- readSMDHeader(fullname)$NHeaderRecords
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, flush = TRUE, ...)
       nspots <- nrow(obj)
   }, {
       skip <- readGenericHeader(fullname, columns = columns, sep =
sep)$NHeaderRecords
       obj <- read.columns(fullname, required.col, text.to.search,
           skip = skip, sep = sep, quote = quote, stringsAsFactors = FALSE,
           fill = TRUE, flush = TRUE, ...)
       nspots <- nrow(obj)
   })
1: read.maimages(targets, source = "genepix", wt.fun = f)

> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_3.2.1

Well, sorry for the extention, but hopefully i cant get an anwser and if this
not the

Greets



Vincent Carey escribió:
> Please read the posting guide.  You did not provide the result of
> sessionInfo().  You may be using an inconvenient locale.  Typically if the
> following holds
>
>> Sys.getlocale()
> [1] "C"
>
> you will not run into the error noted for this task.
>
> On Sun, Apr 4, 2010 at 9:31 PM, <lapereir at uc.cl> wrote:
>
>> Dear list
>>
>> I am getting a couple of erros when trying to  import gpr files using the
>> read.maimages of Limma.
>>
>> > targets<-readTargets("targets.txt")
>> > RG <- read.maimages(targets, source="genepix", wt.fun=f)
>> Error in gsub("\\.", "\\\\.", x) :
>> input string 1 is invalid in this locale
>>
>> I search in R Help for the function of gsub, but i cannot fix the error
>> that
>> give me, so that i cant import any genepix (.gpr) files.
>>
>> Thank
>> Luis
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>


-- 
Luis Pereira
Laboratorio de Farmacología y Bioquímica
Departamento de Biología Celular y Molecular
Facultad de Ciencias Biológicas
Universidad Católica