Hi Denis, you refer to the thread 'Custom Canine SNP' started on July 18, 2008. In KD's message on August 14, 2008 you can see how he explicitly set argument genome="Canine" when he sets up the GLAD model. From the verbose output I can see you are using CBS, but it is not clear how you set it up. Are you doing:
cbs <- CbsModel(ces, genome="Canine")? If not, do that. Then (for troubleshooting purposes only) try df <- getGenomeData(cbs, verbose=verbose); print(df); This latter step will try to load the tab-delimited file containing the information about the number of bases per chromosomes. Since you specify "Canine" above, it will try to locate and read the file: annotationData/genomes/Canine/Canine,chromosomes.txt or any with additional tags, e.g. annotationData/genomes/Canine/Canine,chromosomes,UGP,HB20100822.txt It needs to contain (at least) the two columns "chromosome" and "nbrOfBases". I don't have the exact numbers for the Canine genome, but see the attached file for an example. Feel free to forward the data to me, and I'll add this Canine annotation data so it's built in to the aroma framework. If you get the above working once, then process(ce) should work too. Hope this helps Henrik On Mon, Aug 23, 2010 at 4:28 AM, Denis <amer.ak...@rub.de> wrote: > Hi there, > > I hope you can help me with my problem since I have followed kind help > with a similar problem on the google aroma.affymetrix formus, yet > without the last bit of information I would need to succeed: > http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/96676bd38d64e884/e01329e5f44ba42b?lnk=gst&q=building+ufl+file+for+DogSty06m520431#e01329e5f44ba42b > > > We are processing the DogSty06m520431 chips and my Prof. wants me to > generate CNV calculations for the corresponding samples. So far I > could stick to the helpful guide on the aroma homepage for “Total Copy > Number Analysis (GWS5 & GWS6)”. Yet I am now faced with 2 problems of > which I hope you could give me a hand. > > First one is that when executing the command: > >> process(ce, chromosomes=c(38), verbose=verbose) > > for chromosomes >24 the analyses aborts with following prompting for > e.g. chr25: > >> process(ce, chromosomes=c(25), verbose=verbose) > 20100823 13:05:15|Generating ChromosomeExplorer report... > 20100823 13:05:15| Setting up ChromosomeExplorer report files... > 20100823 13:05:15| Copying template files... > 20100823 13:05:15| Source path: C:/Programme/R/R-2.11.1/library/ > aroma.core/reports/includes > 20100823 13:05:15| Destination path: reports/includes > 20100823 13:05:23| Copying template files...done > 20100823 13:05:23| Setting up ChromosomeExplorer report files...done > 20100823 13:05:23| Explorer output version: 3 > 20100823 13:05:23| Compiling ChromosomeExplorer.onLoad.js.rsp... > 20100823 13:05:23| Source: C:/Programme/R/R-2.11.1/library/aroma.core/ > reports/templates/rsp/ChromosomeExplorer3/ > ChromosomeExplorer.onLoad.js.rsp > 20100823 13:05:23| Output path: reports/Weim/ACC,-XY,AVG,+300,A+B > 20100823 13:05:23| Scanning directories for available chip types... > 20100823 13:05:23| Detected chip types: DogSty06m520431 > 20100823 13:05:23| Scanning directories for available chip > types...done > 20100823 13:05:23| Scanning image files for available zooms... > 20100823 13:05:24| Detected (or default) zooms: 1, 2, 4, 8, 16, 32, > 64 > 20100823 13:05:24| Scanning image files for available zooms...done > 20100823 13:05:24| Scanning directory for subdirectories... > 20100823 13:05:24| Detected (or default) sets: cbs > 20100823 13:05:24| Scanning directory for subdirectories...done > 20100823 13:05:24| Compiling RSP... > member data.class dimension objectSize > 1 chipTypes character 1 72 > 2 chrLayers character 0 24 > 3 sampleLabels character 4 264 > 4 sampleLayers character 0 24 > 5 samples character 4 264 > 6 sets character 1 64 > 7 zooms numeric 7 56 > 20100823 13:05:28| Sample names: > [1] "W24a_(DogSty06m520431)" "W469_(DogSty06m520431)" > "W511_(DogSty06m520431)" > [4] "W513_(DogSty06m520431)" > 20100823 13:05:28| Full sample names: > [1] "W24a_(DogSty06m520431)" "W469_(DogSty06m520431)" > "W511_(DogSty06m520431)" > [4] "W513_(DogSty06m520431)" > 20100823 13:05:28| Compiling RSP...done > 20100823 13:05:29| Compiling ChromosomeExplorer.onLoad.js.rsp...done > Loading required package: RColorBrewer > Loading required package: Cairo > 20100823 13:05:40| Building tuple of reference sets... > 20100823 13:05:40| No reference available. > 20100823 13:05:40| Calculating average copy-number signals... > 20100823 13:05:40| Retrieving average cell signals across 4 > arrays... > CnChipEffectFile: > Name: .average-intensities-median-mad > Tags: f1b4541a56b9bb2404325d6053edc91e > Full name: .average-intensities-median- > mad,f1b4541a56b9bb2404325d6053edc91e > Pathname: plmData/Weim,ACC,-XY,AVG,+300,A+B/ > DogSty06m520431/.average-intensities-median- > mad,f1b4541a56b9bb2404325d6053edc91e.CEL > File size: 4.86 MB (5091526 bytes) > RAM: 0.01 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Timestamp: 2010-08-19 11:56:52 > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > 20100823 13:05:40| Retrieving average cell signals across 4 > arrays...done > 20100823 13:05:41| Calculating average copy-number signals...done > 20100823 13:05:41| Building tuple of reference sets...done > 20100823 13:05:41| Using reference tuple: > CnChipEffectSetTuple: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Chip types: DogSty06m520431 > CnChipEffectSet: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Number of arrays: 4 > Names: .average-intensities-median-mad, .average-intensities-median- > mad, .average-intensities-median-mad, .average-intensities-median-mad > Time period: 2010-08-19 11:56:52 -- 2010-08-19 11:56:52 > Total file size: 19.42MB > RAM: 0.01MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > RAM: 0.00MB > 20100823 13:05:41| Extract DataFileMatrix... > 20100823 13:05:41| Array: 1 > 20100823 13:05:41| Test data sets: > CnChipEffectSetTuple: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Chip types: DogSty06m520431 > CnChipEffectSet: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Number of arrays: 4 > Names: W24a_(DogSty06m520431), W469_(DogSty06m520431), > W511_(DogSty06m520431), W513_(DogSty06m520431) > Time period: 2010-08-19 09:55:50 -- 2010-08-19 09:55:51 > Total file size: 19.42MB > RAM: 0.01MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > RAM: 0.00MB > 20100823 13:05:42| Reference data sets: > CnChipEffectSetTuple: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Chip types: DogSty06m520431 > CnChipEffectSet: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Number of arrays: 4 > Names: .average-intensities-median-mad, .average-intensities-median- > mad, .average-intensities-median-mad, .average-intensities-median-mad > Time period: 2010-08-19 11:56:52 -- 2010-08-19 11:56:52 > Total file size: 19.42MB > RAM: 0.01MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > RAM: 0.00MB > 20100823 13:05:42| Test data files: > $DogSty06m520431 > CnChipEffectFile: > Name: W24a_(DogSty06m520431) > Tags: chipEffects > Full name: W24a_(DogSty06m520431),chipEffects > Pathname: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431/ > W24a_(DogSty06m520431),chipEffects.CEL > File size: 4.86 MB (5091508 bytes) > RAM: 0.01 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Timestamp: 2010-08-19 09:55:50 > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > > attr(,"class") > [1] "AromaUnitTotalCnBinaryFileList" > "GenericDataFileList" > [3] "list" > 20100823 13:05:43| Extract DataFileMatrix...done > 20100823 13:05:43| Genomic-signal tags: > 20100823 13:05:43| Reference tags: 0a3adbbf31c6ac7f1d75cb5aaaaa0aa5 > 20100823 13:05:43| Array #1 ('W24a_(DogSty06m520431)') of 4 on > chromosome 25... > 20100823 13:05:43| Loading results from file... > 20100823 13:05:43| Pathname: cbsData/Weim,ACC,-XY,AVG,+300,A+B/ > DogSty06m520431/ > W24a_(DogSty06m520431),chr25,0a3adbbf31c6ac7f1d75cb5aaaaa0aa5.xdr > 20100823 13:05:43| Fit object: DNAcopy > 20100823 13:05:43| Loading results from file...done > 20100823 13:05:43| Calling onFit.CopyNumberSegmentationModel() > hooks... > ERROR caught in onFit.CopyNumberSegmentationModel(): > [2010-08-23 13:05:44] 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, chromosomes = c(25), verbose = > verbose) > at process(ce, chromosomes = c(25), verbose = verbose) > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 1128467 30.2 1800540 48.1 2345443 62.7 > Vcells 615145 4.7 1853960 14.2 2259172 17.3 > 20100823 13:05:44| Calling onFit.CopyNumberSegmentationModel() > hooks...done > 20100823 13:05:44| Calling onFit.CopyNumberSegmentationModel() > hooks...done > 20100823 13:05:44|Array #1 ('W24a_(DogSty06m520431)') of 4 on > chromosome 25...done > 20100823 13:05:44|Extract DataFileMatrix... > 20100823 13:05:44| Array: 2 > 20100823 13:05:44| Test data sets: > CnChipEffectSetTuple: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Chip types: DogSty06m520431 > CnChipEffectSet: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Number of arrays: 4 > Names: W24a_(DogSty06m520431), W469_(DogSty06m520431), > W511_(DogSty06m520431), W513_(DogSty06m520431) > Time period: 2010-08-19 09:55:50 -- 2010-08-19 09:55:51 > Total file size: 19.42MB > RAM: 0.01MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > RAM: 0.00MB > 20100823 13:05:44| Reference data sets: > CnChipEffectSetTuple: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Chip types: DogSty06m520431 > CnChipEffectSet: > Name: Weim > Tags: ACC,-XY,AVG,+300,A+B > Path: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431 > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Number of arrays: 4 > Names: .average-intensities-median-mad, .average-intensities-median- > mad, .average-intensities-median-mad, .average-intensities-median-mad > Time period: 2010-08-19 11:56:52 -- 2010-08-19 11:56:52 > Total file size: 19.42MB > RAM: 0.01MB > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > RAM: 0.00MB > 20100823 13:05:45| Test data files: > $DogSty06m520431 > CnChipEffectFile: > Name: W469_(DogSty06m520431) > Tags: chipEffects > Full name: W469_(DogSty06m520431),chipEffects > Pathname: plmData/Weim,ACC,-XY,AVG,+300,A+B/DogSty06m520431/ > W469_(DogSty06m520431),chipEffects.CEL > File size: 4.86 MB (5091508 bytes) > RAM: 0.01 MB > File format: v4 (binary; XDA) > Platform: Affymetrix > Chip type: DogSty06m520431,monocell > Timestamp: 2010-08-19 09:55:50 > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, > combineAlleles: logi TRUE) > > attr(,"class") > [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList" > [3] "list" > 20100823 13:05:46|Extract DataFileMatrix...done > 20100823 13:05:46|Genomic-signal tags: > 20100823 13:05:46|Reference tags: 0a3adbbf31c6ac7f1d75cb5aaaaa0aa5 > 20100823 13:05:46|Array #2 ('W469_(DogSty06m520431)') of 4 on > chromosome 25... > RawCopyNumbers: > Name: > Chromosome: 25 > Position range: [3.01577e+06,5.45628e+07] > Number of loci: 3399 > Mean distance between loci: 15169.8 > Loci fields: x [3399xnumeric], y [3399xnumeric] > RAM: 0.05MB > 20100823 13:05:51| Segmenting... > 20100823 13:05:51| Retrieving the fit function... > 20100823 13:05:51| Method: segment > 20100823 13:05:51| Package: DNAcopy v1.22.1 > chr "Function: " > 20100823 13:05:51| Formals: > Dotted pair list of 15 > $ x : symbol > $ weights : NULL > $ alpha : num 0.01 > $ nperm : num 10000 > $ p.method : language c("hybrid", "perm") > $ min.width : num 2 > $ kmax : num 25 > $ nmin : num 200 > $ eta : num 0.05 > $ sbdry : NULL > $ trim : num 0.025 > $ undo.splits: language c("none", "prune", "sdundo") > $ undo.prune : num 0.05 > $ undo.SD : num 3 > $ verbose : num 1 > 20100823 13:05:51| Retrieving the fit function...done > 20100823 13:05:51| Extracting data of interest... > 20100823 13:05:51| Extracting data used by segmentation > algorithms... > 20100823 13:05:51| Sample name: Unnamed sample > 20100823 13:05:51| Chromosome: 25 > 20100823 13:05:51| Number of loci: 3399 > 20100823 13:05:52| Dropping loci with unknown locations... > 20100823 13:05:52| Number of dropped loci: 0 > 20100823 13:05:52| Dropping loci with unknown locations...done > 20100823 13:05:52| Dropping loci with non-finite signals... > 20100823 13:05:52| Number of dropped loci: 0 > 20100823 13:05:52| Dropping loci with non-finite signals...done > 20100823 13:05:52| Order data along genome... > 20100823 13:05:52| Order data along genome...done > 'data.frame': 3399 obs. of 3 variables: > $ chromosome: int 25 25 25 25 25 25 25 25 25 25 ... > $ x : num 3015772 3016146 3023985 3057069 3057086 ... > $ y : num -0.00114 0.01815 0.01767 -0.0586 -0.02699 ... > - attr(*, "sampleName")= chr "Unnamed sample" > 20100823 13:05:52| Extracting data used by segmentation > algorithms...done > 'data.frame': 3399 obs. of 3 variables: > $ chromosome: int 25 25 25 25 25 25 25 25 25 25 ... > $ x : num 3015772 3016146 3023985 3057069 3057086 ... > $ y : num -0.00114 0.01815 0.01767 -0.0586 -0.02699 ... > - attr(*, "sampleName")= chr "Unnamed sample" > 20100823 13:05:52| Extracting data of interest...done > 20100823 13:05:52| Setting up method arguments... > 20100823 13:05:52| Setting up DNAcopy data structure... > Classes ‘CNA’ and 'data.frame': 3399 obs. of 3 variables: > $ chrom :Class 'AsIs' int [1:3399] 25 25 25 25 25 25 25 > 25 25 25 ... > $ maploc : num 3015772 3016146 3023985 3057069 > 3057086 ... > $ Unnamed.sample: num -0.00114 0.01815 0.01767 -0.0586 > -0.02699 ... > - attr(*, "data.type")= chr "logratio" > Classes ‘CNA’ and 'data.frame': 3399 obs. of 3 variables: > $ chrom :Class 'AsIs' int [1:3399] 25 25 25 25 25 25 25 > 25 25 25 ... > $ maploc : num 3015772 3016146 3023985 3057069 > 3057086 ... > $ Unnamed sample: num -0.00114 0.01815 0.01767 -0.0586 > -0.02699 ... > - attr(*, "data.type")= chr "logratio" > 20100823 13:05:52| Setting up DNAcopy data structure...done > 20100823 13:05:52| User and segmentation arguments: > List of 1 > $ plotband: logi TRUE > 20100823 13:05:52| Final arguments: > List of 2 > $ :Classes ‘CNA’ and 'data.frame': 3399 obs. of 3 > variables: > ..$ chrom :Class 'AsIs' int [1:3399] 25 25 25 25 25 25 > 25 25 25 25 ... > ..$ maploc : num [1:3399] 3015772 3016146 3023985 3057069 > 3057086 ... > ..$ Unnamed sample: num [1:3399] -0.00114 0.01815 0.01767 -0.0586 > -0.02699 ... > ..- attr(*, "data.type")= chr "logratio" > $ verbose: logi TRUE > 20100823 13:05:52| Setting up method arguments...done > 20100823 13:05:52| Looking for cached results... > 20100823 13:05:52| Looking for cached results...done > 20100823 13:05:52| Calling segment() of DNAcopy... > 20100823 13:05:52| Captured output that was sent to stdout: > 20100823 13:05:52| Analyzing: Unnamed sample > 20100823 13:05:52| Fitting time (in seconds): > user system elapsed > 0.36 0.00 0.44 > 20100823 13:05:52| Fitting time per 1000 loci (in seconds): > user system elapsed > 0.1059135 0.0000000 0.1294498 > 20100823 13:05:52| Estimating aroma parameters... > 20100823 13:05:52| Estimating aroma parameters...done > 20100823 13:05:52| Results object: > List of 2 > $ data :Classes ‘CNA’ and 'data.frame': 3399 obs. of 3 > variables: > ..$ chrom :Class 'AsIs' int [1:3399] 25 25 25 25 25 25 > 25 25 25 25 ... > ..$ maploc : num [1:3399] 3015772 3016146 3023985 3057069 > 3057086 ... > ..$ Unnamed sample: num [1:3399] -0.00114 0.01815 0.01767 -0.0586 > -0.02699 ... > ..- attr(*, "data.type")= chr "logratio" > $ output:'data.frame': 1 obs. of 6 variables: > ..$ ID : chr "Unnamed sample" > ..$ chrom : int 25 > ..$ loc.start: num 3015772 > ..$ loc.end : num 54562819 > ..$ num.mark : num 3399 > ..$ seg.mean : num -0.0088 > - attr(*, "class")= chr "DNAcopy" > - attr(*, "processingTime")=Class 'proc_time' Named num [1:5] > 0.36 0 0.44 NA NA > .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" > "elapsed" "user.child" ... > - attr(*, "pkgDetails")= chr "DNAcopy v1.22.1" > - attr(*, "aromaEstimates")=List of 2 > ..$ stddevAll : num 0.0639 > ..$ stddevRegions: num 0.000177 > 20100823 13:05:53| Calling segment() of DNAcopy...done > 20100823 13:05:53| Segmenting...done > List of 2 > $ data :Classes ‘CNA’ and 'data.frame': 3399 obs. of 3 > variables: > ..$ chrom :Class 'AsIs' int [1:3399] 25 25 25 25 25 25 25 > 25 25 25 ... > ..$ maploc : num [1:3399] 3015772 3016146 3023985 3057069 > 3057086 ... > ..$ Unnamed sample: num [1:3399] -0.00114 0.01815 0.01767 -0.0586 > -0.02699 ... > ..- attr(*, "data.type")= chr "logratio" > $ output:'data.frame': 1 obs. of 6 variables: > ..$ ID : chr "Unnamed sample" > ..$ chrom : int 25 > ..$ loc.start: num 3015772 > ..$ loc.end : num 54562819 > ..$ num.mark : num 3399 > ..$ seg.mean : num -0.0088 > - attr(*, "class")= chr "DNAcopy" > - attr(*, "processingTime")=Class 'proc_time' Named num [1:5] 0.36 > 0 0.44 NA NA > .. ..- attr(*, "names")= chr [1:5] "user.self" "sys.self" "elapsed" > "user.child" ... > - attr(*, "pkgDetails")= chr "DNAcopy v1.22.1" > - attr(*, "aromaEstimates")=List of 2 > ..$ stddevAll : num 0.0639 > ..$ stddevRegions: num 0.000177 > 20100823 13:05:53| Class of fitted object: DNAcopy > 20100823 13:05:53| Time to fit segmentation model: 0.02min > 20100823 13:05:53| Validate that it can be coerced... > RawCopyNumbers: > Name: > Chromosome: 25 > Position range: [3.01577e+06,5.45628e+07] > Number of loci: 3399 > Mean distance between loci: 15169.8 > Loci fields: x [3399xnumeric], y [3399xnumeric] > RAM: 0.05MB > 20100823 13:05:53| Robust first-order standard deviation estimate: > 0.0639319 > CopyNumberRegions: > Number of regions: 1 > RAM: 0.00MB > 20100823 13:05:53| Validate that it can be coerced...done > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 1128484 30.2 1800540 48.1 2345443 62.7 > Vcells 646387 5.0 2026658 15.5 2259172 17.3 > 20100823 13:05:53| Saving to file... > 20100823 13:05:53| Pathname: cbsData/Weim,ACC,-XY,AVG,+300,A+B/ > DogSty06m520431/ > W469_(DogSty06m520431),chr25,0a3adbbf31c6ac7f1d75cb5aaaaa0aa5.xdr > 20100823 13:05:53| Saving to file...done > 20100823 13:05:53| Total time for chromosome 25: 6.55s == 0.11min > 20100823 13:05:53| Total time per 1000 locus (with 3399 loci): 1.93s/ > locus > 20100823 13:05:53| Fraction of time spent on different tasks: Fitting: > 18.6%, Reading: 75.3%, Writing: 0.8%, Explicit garbage collection: > 4.1% > 20100823 13:05:53| Calling onFit.CopyNumberSegmentationModel() > hooks... > ERROR caught in onFit.CopyNumberSegmentationModel(): > [2010-08-23 13:05:53] 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, chromosomes = c(25), verbose = > verbose) > at process(ce, chromosomes = c(25), verbose = verbose) > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 1128909 30.2 1800540 48.1 2345443 62.7 > Vcells 636568 4.9 2026658 15.5 2259172 17.3 > 20100823 13:05:53| Calling onFit.CopyNumberSegmentationModel() > hooks...done > 20100823 13:05:53|Calling onFit.CopyNumberSegmentationModel() > hooks...done > Fehler in list(`process(ce, chromosomes = c(25), verbose = verbose)` = > <environment>, : > > [2010-08-23 13:05:53] 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, chromosomes = c(25), verbose = > verbose) > at process(ce, chromosomes = c(25), verbose = verbose) > Zusätzlich: Warnmeldung: > In file.remove(file) : > kann Datei 'C:\DOKUME~1\MHG01\LOKALE~1\Temp\Rtmphc5yil > \findGraphicsDevice-testFile63656f75' nicht löschen. Grund 'Permission > denied' > Fehler in list(`process(ce, chromosomes = c(25), verbose = verbose)` = > <environment>, : > > [2010-08-23 13:05:53] 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.ChromosomeExplor > 20100823 13:05:53|Generating ChromosomeExplorer report...done > > > Corresponding session Info: > >> sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] Cairo_1.4-5 RColorBrewer_1.0-2 > DNAcopy_1.22.1 > [4] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 > affxparser_1.20.0 > [7] R.huge_0.2.0 aroma.core_1.7.0 > aroma.light_1.16.1 > [10] matrixStats_0.2.1 R.rsp_0.3.6 > R.cache_0.3.0 > [13] R.filesets_0.8.3 digest_0.4.2 > R.utils_1.5.0 > [16] R.oo_1.7.3 R.methodsS3_1.2.0 > > > > My next problem is that when displaying the CNVs in chromosome > explorer they are in the scale relative to Human chromosomes. > > I have figuered out how to modify the ce option in order to display > all generated images (in the case 39 chromoses were calculated), yet I > think that the two problems are linked together since I cannot figuere > out which reference file is used for the generation of the images > (perhaps when replacing the corresponding file with the one for canine > specific loci (chr and markerposition) then the computation of chr>24 > might also be processed). > > To be honest, since I have little clue about programming, I have no > Idea how to solve this problem and I would be really thankful for your > help. > > > > With great respect for your work and suggestions > > > Yours sincerely > > Denis > > > -- > 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/ > -- 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. 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chromosome nbrOfBases 1 12548891 2 88182672 3 94659212 4 91429679 5 91969480 6 80531300 7 83918830 8 76319553 9 64388646 10 72471775 11 77415697 12 75458181 13 66171193 14 63877078 15 67136955 16 62534543 17 67108084 18 58768331 19 56709702 20 61246656 21 53889065 22 64179564 23 55386667 24 50674002 25 54562819 26 42004589 27 48236582 28 44161646 29 44727140 30 43154895 31 41581023 32 41575543 33 34226766 34 45065038 35 29486428 36 33827475 37 33893929 38 26869798 39 125840674
