Hello there. Does anyone knows how to generate XYS file from nimblegen pair file? I am having a lot of problem trying to do accomplish this and analyze my data thru bioconductor. I have two main errors. One if I try to read xys file a receive this: > 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 OR When i am building annotation package: > makePdInfoPackage(seed, destDir = ".") ====================================================================== ========== Building annotation package for Nimblegen Expression Array NDF: 2006-08-18_TI4932_60mer.ndf XYS: 50186202_532.xys ====================================================================== ========== Parsing file: 2006-08-18_TI4932_60mer.ndf... OK Parsing file: 50186202_532.xys... OK Merging NDF and XYS files... OK Preparing contents for featureSet table... OK Preparing contents for bgfeature table... OK Preparing contents for pmfeature table... OK Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) : Control probe possibly identified as Experimental I know, I Know, this seems to be easy, but I can not understand what is going on!!! Thanks in advance for all of list members for your time reading this. My best regards Marcelo -- 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

Marcelo, do you have access to the NimbleScan software? It is as simple as selecting Report / XYS (or something similar to that) e pointing to the TIFF images for which you want the XYS files. For PAIR -> XYS, please check the following thread: http://comments.gmane.org/gmane.science.biology.informatics.conductor/ 27547 If you still find problems, please contact me off-list... and I'll get back to the list once things work out. b 2010/7/12 Marcelo Brand?o <brandao.marcelo at="" gmail.com="">: > Hello there. > Does anyone knows how to generate XYS file from nimblegen pair file? > I am having a lot of problem trying to do accomplish this and analyze > my data thru bioconductor. > I have two main errors. > One if I try to read xys file a receive this: >> 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 > OR > When i am building annotation package: > >> makePdInfoPackage(seed, destDir = ".") > ==================================================================== ============ > Building annotation package for Nimblegen Expression Array > NDF: 2006-08-18_TI4932_60mer.ndf > XYS: 50186202_532.xys > ==================================================================== ============ > Parsing file: 2006-08-18_TI4932_60mer.ndf... OK > Parsing file: 50186202_532.xys... OK > Merging NDF and XYS files... OK > Preparing contents for featureSet table... OK > Preparing contents for bgfeature table... OK > Preparing contents for pmfeature table... OK > Error in parseNgsPair(object at ndfFile, object at xysFile, verbose = !quiet) : > ?Control probe possibly identified as Experimental > > > I know, I Know, this seems to be easy, but I can not understand what > is going on!!! > > Thanks in advance for all of list members for your time reading this. > > My best regards > > Marcelo > > > -- > 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 >