Hi Hendrik, it works now without error messages! Thanks!
The chromosome explorer looks fine except for chromosomes > 19. There are links for chromosomes 20,21,22 and X in the navigation bar that do not work (since mice do not have chr. 20,21,22). Y and M are not linked. I read in this forum that the links currently are "hard coded". However, this is not a big problem for me. Thanks, Hans-Ulrich On Dec 8, 1:37 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi, > > it looks like the patch wasn't applied. I've actually committed the > bug fix to CRAN where aroma.core v1.8.1 is now available. If you do > > source("http://aroma-project.org/hbLite.R"); > hbInstall("aroma.affymetrix"); > > that one should install (and any patches will be dropped). > > Let me know if you still have problems > > /Henrik > > On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich > > <hans-ulrich.kl...@uni-muenster.de> wrote: > > Hi Hendrik, > > > I installed the patches and removed the report and the cbs folder. > > Then, I run the segmentation and the chromosome explorer again. I got > > the same/similar error message (see below). The error occured when > > processing the second sample so the first one seems to run without > > problems. > > Can I run the chromosome explorer and exclude chromosome 25? > > > Regards, > > Hans-Ulrich > > > 20101206 12:53:52| Plotting S2 for chromosome 24 [NAMB]...done > > 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel() > > hooks...done > > 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 24...done > > 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 25... > > 20101206 12:53:52| Loading results from file... > > 20101206 12:53:52| Pathname: cbsData/Koschmieder,ACC,ra,-XY,BPN,- > > XY,RMA,A+B,FLN,-XY,paired/MOUSEDIVm520650/ > > S2,chr25,9012c8079b8a75fe8fc388ca02bfb65e.xdr > > 20101206 12:53:52| Fit object: DNAcopy > > 20101206 12:53:52| Loading results from file...done > > 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel() > > hooks... > > ERROR caught in onFit.CopyNumberSegmentationModel(): > > [2010-12-06 12:53:53] Exception: Cannot infer number of bases in > > chromosome. No such chromosome: 25 > > at throw(Exception(...)) > > at throw.default("Cannot infer number of bases in chromosome. No > > such chromoso > > at throw("Cannot infer number of bases in chromosome. No such > > chromosome: ", c > > at getChromosomeLength(chromosome) > > at doTryCatch(return(expr), name, parentenv, handler) > > at tryCatchOne(expr, names, parentenv, handlers[[1]]) > > at tryCatchList(expr, classes, parentenv, handlers) > > at tryCatch({ > > at fcn(...) > > at doTryCatch(return(expr), name, parentenv, handler) > > at tryCatchOne(expr, names, parentenv, handlers[[1]]) > > at tryCatchList(expr, classes, parentenv, handlers) > > at tryCatch({ > > at callHooks.list(hooks, ...) > > at callHooks(hooks, ...) > > at callHooks.default(hookName, fit = fit, chromosome = chr, fullname > > = fullnam > > at callHooks(hookName, fit = fit, chromosome = chr, fullname = > > fullname) > > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, > > verbose = v > > at fit(this, ..., .retResults = FALSE, verbose = verbose) > > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat > > = "png", p > > at plot(model, path = path, imageFormat = "png", plotband = > > plotband, arrays = > > at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes > > = chromos > > at writeGraphs(this, arrays = arrays, chromosomes = chromosomes, > > zooms = zooms > > at process.ChromosomeExplorer(ce, verbose = verbose) > > at process(ce, verbose = verbose) > > used (Mb) gc trigger (Mb) max used (Mb) > > Ncells 1178686 63 4079505 217.9 26615696 1421.5 > > Vcells 1568318 12 4818496 36.8 41974408 320.3 > > 20101206 12:53:53| Calling onFit.CopyNumberSegmentationModel() > > hooks...done > > 20101206 12:53:53|Calling onFit.CopyNumberSegmentationModel() > > hooks...done > > Error in list(`process(ce, verbose = verbose)` = <environment>, > > `process.ChromosomeExplorer(ce, verbose = verbose)` = > > <environment>, : > > > [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent' > > makes 'indentPos' negative: -1 > > at throw(Exception(...)) > > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: > > at throw("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: ", this > > at exit.Verbose(verbose) > > at exit(verbose) > > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, > > verbose = v > > at fit(this, ..., .retResults = FALSE, verbose = verbose) > > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat > > = "png", p > > at plot(model, path = path, imageFormat = "png", plotband = > > plotband, arrays = > > at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes > > = chromos > > at writeGraphs(this, arrays = arrays, chromosomes = chromosomes, > > zooms = zooms > > at process.ChromosomeExplorer(ce, verbose = verbose) > > at process(ce, verbose = verbose) > > Error in list(`process(ce, verbose = verbose)` = <environment>, > > `process.ChromosomeExplorer(ce, verbose = verbose)` = > > <environment>, : > > > [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent' > > makes 'indentPos' negative: -1 > > at throw(Exception(...)) > > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: > > at throw("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: ", this > > at exit.Verbose(this) > > at exit(this) > > at popState.Verbose(verbose) > > at popState(verbose) > > at throw.Exception(Exception(...)) > > at throw(Exception(...)) > > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: > > at throw("Cannot exit(): Argument 'indent' makes 'indentPos' > > negative: ", this > > at exit.Verbose(verbose) > > at exit(verbose) > > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, > > verbose = v > > at fit(this, ..., .retResults = FALSE, verbose = verbose) > > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat > > = "png", p > > at plot(model, path = path, imageFormat = "png", plotband = > > plotband, arrays = > > at writeGraphs.ChromosomeExplore > > 20101206 12:53:53|Generating ChromosomeExplorer report...done > > > On Dec 3, 8:09 am, Henrik Bengtsson <henrik.bengts...@aroma- > > project.org> wrote: > >> Hi, > > >> I could reproduce this error (also on the Human genome when trying to > >> generate CE plots for Chr25). It's a bug, which I have patched (until > >> next release). Run the following and the patches will be installed > >> too: > > >> source("http://aroma-project.org/hbLite.R"); > >> hbInstall("aroma.affymetrix"); > > >> Let me know if it solves your problem. > > >> /Henrik > > >> On Wed, Dec 1, 2010 at 2:28 PM, Hans-Ulrich > > >> <hans-ulrich.kl...@uni-muenster.de> wrote: > >> > Sorry, I forgot that: > > >> >> sessionInfo() > >> > R version 2.12.0 (2010-10-15) > >> > Platform: x86_64-pc-linux-gnu (64-bit) > > >> > locale: > >> > [1] C > > >> > attached base packages: > >> > [1] stats graphics grDevices utils datasets methods > >> > base > > >> > other attached packages: > >> > [1] Cairo_1.4-5 RColorBrewer_1.0-2 > >> > DNAcopy_1.24.0 > >> > [4] preprocessCore_1.12.0 sfit_0.1.9 > >> > aroma.affymetrix_1.8.1 > >> > [7] aroma.apd_0.1.7 affxparser_1.22.0 > >> > R.huge_0.2.0 > >> > [10] aroma.core_1.8.0 aroma.light_1.18.2 > >> > matrixStats_0.2.2 > >> > [13] R.rsp_0.4.0 R.cache_0.3.0 > >> > R.filesets_0.9.1 > >> > [16] digest_0.4.2 R.utils_1.5.8 > >> > R.oo_1.7.4 > >> > [19] R.methodsS3_1.2.1 > > >> > loaded via a namespace (and not attached): > >> > [1] tools_2.12.0 > >> > Warning message: > >> > 'DESCRIPTION' file has 'Encoding' field and re-encoding is not > >> > possible > > >> > Regards, > >> > Hans-Ulrich > > >> > On Dec 1, 6:44 pm, Henrik Bengtsson <henrik.bengts...@aroma- > >> > project.org> wrote: > >> >> Hi, > > >> >> before anything else, are you running the latest aroma.affymetrix > >> >> (v1.8.0), i.e. what's your sessionInfo()? > > >> >> /Henrik > > >> >> On Wed, Dec 1, 2010 at 9:32 AM, Hans-Ulrich > > >> >> <hans-ulrich.kl...@uni-muenster.de> wrote: > >> >> > Hi Hendrik, > > >> >> > I created a file for the mouse genome. However, I still get an error > >> >> > message: > > >> >> >> cbs = CbsModel(cesNSamples, cesNControls, genome="Mouse") > >> >> >> df <- getGenomeData(cbs, verbose=verbose) > >> >> > 20101201 14:44:53|Reading genome chromosome annotation file... > >> >> > 20101201 14:44:53| Searching for the file... > >> >> > 20101201 14:44:54| Searching for the file...done > >> >> > 20101201 14:44:54| Reading data file... > >> >> > 20101201 14:44:54| Pathname: annotationData/genomes/Mouse/ > >> >> > Mouse,chromosomes.txt > >> >> > 20101201 14:44:54| Reading data file...done > >> >> > 20101201 14:44:54| Translating chromosome names... > >> >> > 20101201 14:44:54| Translating chromosome names...done > >> >> > 20101201 14:44:54|Reading genome chromosome annotation file...done > >> >> >> df > >> >> > nbrOfBases nbrOfGenes > >> >> > 1 197195432 1237 > >> >> > 2 181748087 1779 > >> >> > 3 159599783 1046 > >> >> > 4 155630120 1286 > >> >> > 5 152537259 1285 > >> >> > 6 149517037 1158 > >> >> > 7 152524553 1975 > >> >> > 8 131738871 1082 > >> >> > 9 124076172 1260 > >> >> > 10 129993255 1036 > >> >> > 11 121843856 1606 > >> >> > 12 121257530 712 > >> >> > 13 120284312 850 > >> >> > 14 125194864 860 > >> >> > 15 103494974 823 > >> >> > 16 98319150 679 > >> >> > 17 95272651 1075 > >> >> > 18 90772031 522 > >> >> > 19 61342430 739 > >> >> > 23 166650296 800 > >> >> > 24 15902555 12 > >> >> > M 16299 13 > >> >> >> fit(cbs, min.width=5, verbose=verbose) > >> >> >> ce = ChromosomeExplorer(cbs) > >> >> >> process(ce, verbose=verbose) > >> >> > [...] > >> >> > ERROR caught in onFit.CopyNumberSegmentationModel(): > >> >> > [2010-12-01 18:18:04] Exception: Cannot infer number of bases in > >> >> > chromosome. No such chromosome: 25 > >> >> > at throw(Exception(...)) > >> >> > at throw.default("Cannot infer number of bases in chromosome. No > >> >> > such chromoso > >> >> > at throw("Cannot infer number of bases in chromosome. No such > >> >> > chromosome: ", c > >> >> > at getChromosomeLength(chromosome) > >> >> > at doTryCatch(return(expr), name, parentenv, > > ... > > read more » -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/