Custom Canine SNP (DogSty06m520431); problem with chr24-39

[Denis]

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

[Henrik Bengtsson]

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

> --
> 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-af...@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

[Denis]

Hi Henrik,

Sorry for the delay, I had some difficulties in getting GLAD strated
(including gsl ...).
What should I else say than your the best and thank you very much for
your help. I finally got it. I would like to provide you with a
finallized version of the Canine,chromosomes.txt including the band
pattern for your aroma-project.
If you could give me a hint how to manage this (with respect to what
information and column heading are necessary) I would start asap and
attach it hopefully to the next reply :).

Cheers

Denis

[Denis]

sry for some typos was a bit of in a hurry

Denis :)

[Henrik Bengtsson]

Hi,

I missed that you were asking for more help here. If you could send
me a tab-delimited text file with two columns 'chromosome' and
'nbrOfBases', where the chromosome column should contain chromosome
indices (integers) and the nbrOfBases column the number of
nucleotides/length of that chromosome (integer), that would be great
and I add it to the package. Here is an example of what it should
look like:

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

/Henrik

>
> Cheers