[BioC] Error with read.maimages
lapereir at uc.cl
lapereir at uc.cl
Wed Apr 7 17:33:22 CEST 2010
Hi!
Now i realize what Vincent tell me (sory!). I did it and it works!!!, very
thanks.
But i dont have any idea what was the problem, if you are to kind, could you
send me a web page or tutorial web page to explain the problem, it doest
matter if i have to read a lot.
Well, here it the result:
> RG <- read.maimages(targets, source="genepix")
Read GSM307461.gpr
Read GSM307462.gpr
Read GSM307464.gpr
Read GSM307465.gpr
Read GSM307466.gpr
Thanks, for all.
Luis
Martin Morgan escribió:
> Hi Luis --
>
> On 04/05/2010 09:10 AM, lapereir at uc.cl wrote:
>> 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"
>
> I think the suggestion was to change this like
>
>> Sys.setlocale(locale="C")
> [1]
> "LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"
>
> I think this will work on your operating system, but it may be necessary
> to start R in the correct locale.
>
> Martin
>
>
>>> 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
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>
>>
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
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