Hello, We are trying to load Nimblegen Files to the Oligo Package. We do not have .xys files so tried to make them from the .pair files following this link: http://permalink.gmane.org/gmane.science.biology.informatics.conductor /29947 However, when trying to read them into Oligo we get this error > 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 I guess we do not have the .xys files made correctly, but I'm not sure what we have incorrect, since I can't find exactly what it should look like. This is what we have: # software=NimbleScan version=2.4.27 designname=090717_Athal_TAIR9_exp X Y EOL Count 23 3 731.67 NA 135 3 317.33 NA 137 3 742.44 NA 139 3 264.89 NA 141 3 2006.22 NA 143 3 898.11 NA Does anyone see anything obvious we have wrong? Session info is below Any advice would be appreciated. Thanks very much! Colleen > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.090717.athal.tair9.exp_0.0.1 RSQLite_0.9-2 [3] DBI_0.2-5 oligo_1.14.0 [5] oligoClasses_1.12.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affxparser_1.22.0 affyio_1.18.0 Biostrings_2.18.0 [4] IRanges_1.8.0 preprocessCore_1.12.0 splines_2.12.0 >

Hi Coleen I just have the same problem. I wrote an perl script to produce tha xys file using the pair files and the ngd file. I am now away from my lab, if you are interested I may send it to you. Cheers Marcelo —— Marcelo Mendes Brandão http://bioinfo.esalq.usp.br skype: mmbrand via Android Em out 22, 2010 8:57 PM, "Colleen Doherty" <cdoherty@ucsd.edu>escreveu: Hello, We are trying to load Nimblegen Files to the Oligo Package. We do not have .xys files so tried to make them from the .pair files following this link: http://permalink.gmane.org/gmane.science.biology.informatics.conductor /29947 However, when trying to read them into Oligo we get this error > 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 I guess we do not have the .xys files made correctly, but I'm not sure what we have incorrect, since I can't find exactly what it should look like. This is what we have: # software=NimbleScan version=2.4.27 designname=090717_Athal_TAIR9_exp X Y EOL Count 23 3 731.67 NA 135 3 317.33 NA 137 3 742.44 NA 139 3 264.89 NA 141 3 2006.22 NA 143 3 898.11 NA Does anyone see anything obvious we have wrong? Session info is below Any advice would be appreciated. Thanks very much! Colleen > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.090717.athal.tair9.exp_0.0.1 RSQLite_0.9-2 [3] DBI_0.2-5 oligo_1.14.0 [5] oligoClasses_1.12.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affxparser_1.22.0 affyio_1.18.0 Biostrings_2.18.0 [4] IRanges_1.8.0 preprocessCore_1.12.0 splines_2.12.0 > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

The best thing to do is to go back to NimbleScan and generate the reports using the XYS format. b On 22 October 2010 23:56, Colleen Doherty <cdoherty at="" ucsd.edu=""> wrote: > Hello, > ?We are trying to load Nimblegen Files to the Oligo Package. ?We do > not have .xys files so tried to make them from the .pair files > following this link: > http://permalink.gmane.org/gmane.science.biology.informatics.conduct or/29947 > However, when trying to read them into Oligo we get this error > >> 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 > > I guess we do not have the .xys files made correctly, but I'm not sure > what we have incorrect, since I can't find exactly what it should look > like. > This is what we have: > > # software=NimbleScan ? version=2.4.27 designname=090717_Athal_TAIR9_exp > X ? ? ? Y ? ? ? EOL ? ? Count > 23 ? ? ?3 ? ? ? 731.67 ?NA > 135 ? ? 3 ? ? ? 317.33 ?NA > 137 ? ? 3 ? ? ? 742.44 ?NA > 139 ? ? 3 ? ? ? 264.89 ?NA > 141 ? ? 3 ? ? ? 2006.22 NA > 143 ? ? 3 ? ? ? 898.11 ?NA > > Does anyone see anything obvious we have wrong? > Session info is below > Any advice would be appreciated. > Thanks very much! > Colleen > > > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] pd.090717.athal.tair9.exp_0.0.1 RSQLite_0.9-2 > [3] DBI_0.2-5 ? ? ? ? ? ? ? ? ? ? ? oligo_1.14.0 > [5] oligoClasses_1.12.0 ? ? ? ? ? ? Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.22.0 ? ? affyio_1.18.0 ? ? ? ? Biostrings_2.18.0 > [4] IRanges_1.8.0 ? ? ? ? preprocessCore_1.12.0 splines_2.12.0 >> > > _______________________________________________ > 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 >