Dear Henrik,
I deleted reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ and all its
subdirectories. Then did: process(ce, arrays=1, chromosomes=19, verbose=-20)
and here is the entire output:
Generating ChromosomeExplorer report...
Setting up ChromosomeExplorer report files...
Copying template files...
Source path: C:/Program/R/R-2.9.0/library/aroma.core/reports/includes
Destination path: reports/includes
Copying template files...done
Setting up ChromosomeExplorer report files...done
Copying ChromosomeExplorer.html...
Source pathname:
C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html
Destination pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/ChromosomeExplorer.html
Copying ChromosomeExplorer.html...done
Explorer output version: 3
Compiling ChromosomeExplorer.onLoad.js.rsp...
Source:
C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
Output path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Scanning directories for available chip types...
Detected chip types: GenomeWideSNP_6
Scanning directories for available chip types...done
Scanning image files for available zooms...
Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64, 128
Scanning image files for available zooms...done
Scanning directory for subdirectories...
Detected (or default) sets: cbs
Scanning directory for subdirectories...done
Compiling RSP...
Compiling RSP...done
Compiling ChromosomeExplorer.onLoad.js.rsp...done
Loading required package: Cairo
Building tuple of reference sets...
No reference available.
Calculating average chip effects...
Retrieving average cell signals across 28 arrays...
CnChipEffectFile:
Name: .average-intensities-median-mad
Tags: efde1e008fb579a08aa5cda998829722
Full name:
.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722
Pathname:
plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722.CEL
File size: 26.95 MB (28258317 bytes)
RAM: 0.01 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Timestamp: 2009-06-09 15:53:34
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
Retrieving average cell signals across 28 arrays...done
Calculating average chip effects...done
Building tuple of reference sets...done
Using reference tuple:
ChipEffectSetTuple:
Name: CLP
Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Chip types: GenomeWideSNP_6
CnChipEffectSet:
Name: CLP
Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Number of arrays: 28
Names: .average-intensities-median-mad,
.average-intensities-median-mad, ..., .average-intensities-median-mad
Time period: 2009-06-09 15:53:34 -- 2009-06-09 15:53:34
Total file size: 754.58MB
RAM: 0.03MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
RAM: 0.00MB
Chip-effect tags:
Reference tags: 8b8a924f5c9bdfda0388908c4f526ac6
Array #1 ('MP01_LKG12') of 1 on chromosome 19...
Loading results from file...
Pathname:
cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/MP01_LKG12,chr19,8b8a924f5c9bdfda0388908c4f526ac6.xdr
Fit object: DNAcopy
Loading results from file...done
Calling onFit.CopyNumberSegmentationModel() hooks...
Plotting MP01_LKG12 for chromosome 19 [63.79MB]...
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0001.png
Dimensions: 291x400
Ticks by: 1.000000
Plotting graph...
Loading required package: GLAD
[1] "Have fun with GLAD"
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0002.png
Dimensions: 483x400
Ticks by: 1.000000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0004.png
Dimensions: 865x400
Ticks by: 1.000000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0008.png
Dimensions: 1631x400
Ticks by: 1.000000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0016.png
Dimensions: 3162x400
Ticks by: 0.100000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0032.png
Dimensions: 6224x400
Ticks by: 0.100000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0064.png
Dimensions: 12348x400
Ticks by: 0.100000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
Pathname:
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/MP01_LKG12,chr19,x0128.png
Dimensions: 24596x400
Ticks by: 0.010000
Plotting graph...
<simpleError in loadNamespace(name): there is no package called
'RColorBrewer'>
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 501451 13.4 818163 21.9 818163 21.9
Vcells 964929 7.4 7116089 54.3 8718065 66.6
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting graph...done
Plotting MP01_LKG12 for chromosome 19 [63.79MB]...done
Calling onFit.CopyNumberSegmentationModel() hooks...done
Array #1 ('MP01_LKG12') of 1 on chromosome 19...done
Explorer output version: 3
Compiling ChromosomeExplorer.onLoad.js.rsp...
Source:
C:/Program/R/R-2.9.0/library/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
Output path: reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Scanning directories for available chip types...
Detected chip types: GenomeWideSNP_6
Scanning directories for available chip types...done
Scanning image files for available zooms...
Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64, 128
Scanning image files for available zooms...done
Scanning directory for subdirectories...
Detected (or default) sets: cbs
Scanning directory for subdirectories...done
Compiling RSP...
Compiling RSP...done
Compiling ChromosomeExplorer.onLoad.js.rsp...done
Writing CN regions...
Array #1 ('MP01_LKG12') of 1...
Extracting regions from all fits...
Obtaining CN model fits (or fit if missing)...
Building tuple of reference sets...
No reference available.
Calculating average chip effects...
Retrieving average cell signals across 28 arrays...
CnChipEffectFile:
Name: .average-intensities-median-mad
Tags: efde1e008fb579a08aa5cda998829722
Full name:
.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722
Pathname:
plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/.average-intensities-median-mad,efde1e008fb579a08aa5cda998829722.CEL
File size: 26.95 MB (28258317 bytes)
RAM: 0.01 MB
File format: v4 (binary; XDA)
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Timestamp: 2009-06-09 15:53:34
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
Retrieving average cell signals across 28 arrays...done
Calculating average chip effects...done
Building tuple of reference sets...done
Using reference tuple:
ChipEffectSetTuple:
Name: CLP
Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Chip types: GenomeWideSNP_6
CnChipEffectSet:
Name: CLP
Tags: ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Path: plmData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Number of arrays: 28
Names: .average-intensities-median-mad,
.average-intensities-median-mad, ..., .average-intensities-median-mad
Time period: 2009-06-09 15:53:34 -- 2009-06-09 15:53:34
Total file size: 754.58MB
RAM: 0.03MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
RAM: 0.00MB
Chip-effect tags:
Reference tags: 8b8a924f5c9bdfda0388908c4f526ac6
Array #1 ('MP01_LKG12') of 1 on chromosome 19...
Loading results from file...
Pathname:
cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/MP01_LKG12,chr19,8b8a924f5c9bdfda0388908c4f526ac6.xdr
Fit object: DNAcopy
Loading results from file...done
Calling onFit.CopyNumberSegmentationModel() hooks...
Calling onFit.CopyNumberSegmentationModel() hooks...done
Array #1 ('MP01_LKG12') of 1 on chromosome 19...done
Obtaining CN model fits (or fit if missing)...done
Extracting regions for chromosome #19...
Extracting regions for chromosome #19...done
Extracted regions:
'data.frame': 9 obs. of 5 variables:
$ chromosome: int 19 19 19 19 19 19 19 19 19
$ start : num 41911 19748108 40163133 49033800 49744084 ...
$ stop : num 19746740 40162854 49033180 49743930 56705958 ...
$ mean : num 0.1123 0.0474 0.0909 -0.01 0.1035 ...
$ count : int 8887 8182 4739 554 3291 1697 1002 1811 136
Extracting regions from all fits...done
Pathname:
cbsData/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/CLP,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY,regions.xls
Array #1 ('MP01_LKG12') of 1...done
Writing CN regions...done
Generating ChromosomeExplorer report...done
[1] TRUE
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, :
there is no package called 'Cairo'
2: In method(static, ...) :
Ghostscript not found. Searched directories: C:/gs, C:\Program/gs,
/gs, C:\Program\Delade filer/gs
>
And the PNG in
reports/CLP/ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/GenomeWideSNP_6/cbs/
are all as before!!!
Myriam
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