Hi Tim,

Thank you for your response. Actually, my problem was entirely my fault
because I misspecified an argument for methylumIDAT.

So by replacing this line:

> lumi450k<-methylumIDAT(barcodes,getwd())
>

By this:

> lumi450k<-methylumIDAT(barcodes,idatPath=getwd())
>

The function work correctly.

But if my question has permitted finding a bug, it's a good thing.

I have another question, my IDAT files are in different folders and when I
give a vector of these different folders as idatPath argument, the function
returns an error. I don't know if it's a feature or an bug. Do you have an
idea?
I have worked around this problem by placing all my IDAT files in the same
folder but it can be useful to keep all IDAT files in different folders.

Regards,
Dylan




2012/2/16 Tim Triche, Jr. <tim.triche@gmail.com>

> Hi Dylan,
>
> I just realized this is a trivial fix (to a stupid bug introduced late).
>
> For you:
>
> samples = as.data.frame(barcodes)
> mlumi450k<-methylumIDAT(samples) # default is wd
>
> Oddly enough, if I just feed it a character *vector* things work out fine.
> I don't suppose you are feeding it a character *matrix* instead of a
> data.frame?
> A quick test case with 2.1.15 (granted this is NOT the release version)
> succeeded with either a data.frame OR a vector.
>
> For me:
>
> I will patch back in this very obvious bit of functionality and get it
> pushed to SVN.  It's not much to ask :-)
>
>
> Thanks much for reporting it, sorry I did not post a fix sooner (was
> presenting yesterday).
>
> Regards,
>
> --t
>
>
>
> On Tue, Feb 14, 2012 at 2:07 AM, Dylan Aļssi [guest] <
> guest@bioconductor.org> wrote:
>
>>
>> Dear all,
>> I get the following error when I try to load IDAT files with function
>> methylumIDAT:
>>
>> > lumi450k<-methylumIDAT(barcodes,getwd())
>> 0 HumanMethylation27 samples found
>> 24 HumanMethylation450 samples found
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "pData<-", for signature
>> "MethyLumiSet", "character"
>> > traceback()
>> 4: stop("unable to find an inherited method for function \"", fdef@generic
>> ,
>>       "\", for signature ", cnames)
>> 3: function (classes, fdef, mtable)
>>   {
>>       methods <- .findInheritedMethods(classes, fdef, mtable)
>>       if (length(methods) == 1L)
>>           return(methods[[1L]])
>>       else if (length(methods) == 0L) {
>>           cnames <- paste("\"", sapply(classes, as.character),
>>               "\"", sep = "", collapse = ", ")
>>           stop("unable to find an inherited method for function \"",
>>               fdef@generic, "\", for signature ", cnames)
>>       }
>>       else stop("Internal error in finding inherited methods; didn't
>> return a unique method")
>>   }(list("MethyLumiSet", "character"), function (object, value)
>>   standardGeneric("pData<-"), <environment>)
>> 2: `pData<-`(`*tmp*`, value = "C:/Documents and
>> Settings/DylanA/Desktop/samples")
>> 1: methylumIDAT(barcodes, getwd())
>>
>> Anyone have a solution?
>> Thank you.
>>
>> Dylan
>>
>>  -- output of sessionInfo():
>>
>> R version 2.14.1 (2011-12-22)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
>>  LC_MONETARY=French_France.1252
>> [4] LC_NUMERIC=C                   LC_TIME=French_France.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] BiocInstaller_1.2.1                   matrixStats_0.4.3
>>  [3] R.methodsS3_1.2.1
>> IlluminaHumanMethylation450k.db_1.4.6
>>  [5] org.Hs.eg.db_2.6.4                    RSQLite_0.11.1
>>  [7] DBI_0.2-5                             AnnotationDbi_1.16.15
>>  [9] methylumi_2.0.13                      Biobase_2.14.0
>>
>> loaded via a namespace (and not attached):
>> [1] annotate_1.32.1 grid_2.14.1     IRanges_1.12.6  lattice_0.20-0
>>  tools_2.14.1    xtable_1.7-0
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
>
>
> --
> *A model is a lie that helps you see the truth.*
> *
> *
> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>

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