[BioC] Error importing XYS

[Benilton Carvalho]

NimbleGen's software (NimbleScan) does provide you with means of
creating XYS files directly from the TIFF images.

I'm pretty sure the problem is how you created the XYS files. They
must be sorted by X/Y coordinates.

Cheers,

benilton

2010/7/8 Marcelo Brandão <brandao.marcelo at gmail.com>:
> Hi there
> I am trying to analyze nimblegen microarray. Well, everything runs
> smoothly until import the XYS files.
> Here is my first question: I made may xys from .pair files, is it
> correct? Anyone knows if Nimblegen deliver xys files?
> Ok, continuing. When I try to import the XYS file this happens:
> Platform design info loaded.
> Checking designs for each XYS file... Done.
> Allocating memory... Error in smartReadXYS(filenames, sampleNames) :
>  negative extents to matrix
>
> Any clues?
>
> My best regards for all
>
>
> PS: Here is my entire pipeline.
>
>>source("http://bioconductor.org/biocLite.R")
>>library(pdInfoBuilder)
>>filename_ndf <- list.files('.',pattern='.ndf',full.names=T)
>>filename_xys <- list.files('.',pattern=".xys",full.names=T)[1]
>>seed <- new("NgsExpressionPDInfoPkgSeed", ndfFile=filename_ndf, xysFile=filename_xys,
>            author="Marcelo Brandao",email="mmbrand at usp.br",
>            biocViews="AnnotationData", genomebuild="Unknown",
>            url="http://bioinfo.esalq.usp.br")
>>makePdInfoPackage(seed, destDir = ".")
>
> Quit R
>
> R CMD INSTALL  pd.2006.08.18.ti4932.60mer
>
> Back to R
>>source("http://bioconductor.org/biocLite.R")
>>library(oligo)
>>library(pd.2006.08.18.ti4932.60mer)
>>xys_files <- list.xysfiles(full.names=TRUE)
>>dat <- read.xysfiles(xys_files)
> Platform design info loaded.
> Checking designs for each XYS file... Done.
> Allocating memory... Error in smartReadXYS(filenames, sampleNames) :
>  negative extents to matrix
>>
>
> --
> Marcelo Mendes Brandão
> Postdoc fellow
> Laboratório de Biologia Molecular de Plantas - ESALQ/USP
> Website: http://bioinfo.esalq.usp.br
> AtPIN: http://bioinfo.esalq.usp.br/atpin
> SKYPE: mmbrand
> Tel: (+55) 19 3429 4442
>
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