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. 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