[BioC] Error importing XYS

[Marcelo Brandão]

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