Hi Yadav,
thanks for reporting on this. It to me a while to reproduce it. A
quick fix would be to explicitly load the R.cache package, which is
the package that defines that missing getChecksum(). However, I've
fixed this in aroma.core v2.9.2, so you update the error should go
away. Update as usual by:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Let me know if this solves you problem.
Henrik
On Wed, May 22, 2013 at 10:10 AM, <ysapk...@ualberta.ca> wrote:
> Hello,
>
> I am running crmav2 to analyze the copy number data for 680 samples. I setup
> a CBS model but I can not actually do the segmentation and keep on getting
> the following. Any help in this regard would be much appreciated.
>
> print(sm)
> CbsModel:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired
> Chip type (virtual): GenomeWideSNP_6
> Path:
> cbsData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6
> Number of chip types: 1
> Sample & reference file pairs:
> Chip type #1 ('GenomeWideSNP_6') of 1:
> Sample data set:
> AromaUnitTotalCnBinarySet:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 680
> Names: 00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0,
> 00002_GT2_BC_6.0A5_AUG_07_08_MA_0,
> 00002_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ...,
> 01428_MT1428_BD_6.0D11_NOV13_09_YS [680]
> Path (to the first file):
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 4880.69 MB
> RAM: 0.86MB
> Reference: <median of samples>
> RAM: 0.00MB
>
> fit (sm, verbose=-10)
> Building tuple of reference sets...
> Type of reference: median
> No reference available.
> Calculating average copy-number signals...
> Retrieving average unit signals across 680 arrays...
> AromaUnitTotalCnBinaryFile:
> Name: .average-signals-median-mad
> Tags: 91abb70668ff3b542cb5388901c5246a
> Full name: .average-signals-median-mad,91abb70668ff3b542cb5388901c5246a
> Pathname:
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,91abb70668ff3b542cb5388901c5246a.asb
> File size: 7.18 MB (7526027 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20130521 13:55:14
> MDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcDetails><nbrOfFiles>680</nbrOfFiles><checkSum>1e2e97361b53a44049c75e534a73bad1</checkSum></srcDetails><params><meanName>median</meanName><sdName>mad</sdName></params>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
> Retrieving average unit signals across 680 arrays...done
> Calculating average copy-number signals...done
> Building tuple of reference sets...done
> Using reference tuple:
> AromaUnitTotalCnBinarySetTuple:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 680
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [680]
> Path (to the first file):
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 4880.62 MB
> RAM: 0.86MB
> RAM: 0.00MB
> Extract DataFileMatrix...
> Array: 1
> Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 680
> Names: 00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0,
> 00002_GT2_BC_6.0A5_AUG_07_08_MA_0,
> 00002_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ...,
> 01428_MT1428_BD_6.0D11_NOV13_09_YS [680]
> Path (to the first file):
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 4880.69 MB
> RAM: 0.86MB
> RAM: 0.00MB
> Test data files:
> $`GenomeWideSNP_6,Full`
> AromaUnitTotalCnBinaryFile:
> Name: 00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0
> Tags: total
> Full name: 00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total
> Pathname:
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total.asb
> File size: 7.18 MB (7526135 bytes)
> RAM: 0.00 MB
> Number of data rows: 1881415
> File format: v1
> Dimensions: 1881415x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20130521 12:05:44
> MDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6,Full</chipType><srcFile><srcDataSet>caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY</srcDataSet><srcChipType>GenomeWideSNP_6,Full,monocell</srcChipType><srcFullName>00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0,chipEffects</srcFullName><srcChecksum>ff3b69c69012e56c59ab9b08b0e2616d</srcChecksum></srcFile>
> Platform: Affymetrix
> Chip type: GenomeWideSNP_6,Full
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> [3] "list"
> Type of reference: median
> Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Chip types: GenomeWideSNP_6
> AromaUnitTotalCnBinarySet:
> Name: caseControl
> Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
> Number of files: 680
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [680]
> Path (to the first file):
> totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
> Total file size: 4880.62 MB
> RAM: 0.86MB
> RAM: 0.00MB
> Extract DataFileMatrix...done
> Genomic-signal tags: total
> Reference tags: e265cdb12d4460a2793b7cf96278b506
> Array #1 ('00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0') of 680 on chromosome 1...
> Error in UseMethod("getChecksum") :
> no applicable method for 'getChecksum' applied to an object of class
> "list"
> Array #1 ('00001_BM01-1_BC_6.0B4_AUG_19_08_MA_0') of 680 on chromosome
> 1...done
>
> traceback()
> 5: getChecksum(key)
> 4: extractRawCopyNumbers.CopyNumberChromosomalModel(this, array = array,
> chromosome = chr, ...)
> 3: extractRawCopyNumbers(this, array = array, chromosome = chr,
> ...)
> 2: fit.CopyNumberSegmentationModel(sm, verbose = -10)
> 1: fit(sm, verbose = -10)
>
> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
> [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] DNAcopy_1.32.0 aroma.affymetrix_2.9.0 aroma.apd_0.2.3
> [4] R.huge_0.4.1 aroma.light_1.28.0 aroma.core_2.9.0
> [7] matrixStats_0.8.1 R.rsp_0.8.2 R.devices_2.2.2
> [10] R.filesets_2.0.1 R.utils_1.23.2 R.oo_1.13.0
> [13] R.methodsS3_1.4.2 affxparser_1.30.2 BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.3 PSCBS_0.34.8 R.cache_0.6.5 tools_2.15.1
>
> Am I missing something here?
>
> Regards,
> Yadav Sapkota, PhD
> University of Alberta
>
> --
> --
> 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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--
--
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/.
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