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 Brand?o Postdoc fellow Laborat?rio 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

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 Brand?o <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 Brand?o > Postdoc fellow > Laborat?rio 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 > > _______________________________________________ > 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 >