Hi.
On Fri, May 18, 2012 at 11:17 AM, sean nj <njs...@gmail.com> wrote:
> Hi, it's me again :)
>
> I have some level 2 TCGA agilent CGH 244A data, the text files of log2
> ratios. I followed vignettes (http://aroma-project.org/node/43 and
> http://www.aroma-project.org/node/88) and created UGP files and data files
> (asb files) containing log2 CN ratios. But I got the error when I ran CBS
> computing by > fit(sm, verbose=-10). Basically it complianed that there are
> too many non-finite values on chromosome 1 of assay sample 1:
> Array #1 ('MSK_00001_251469322729') of 6 on chromosome 1...
> Error in getRawCnData.CopyNumberChromosomalModel(this, ceList =
> ceList, :
>
> [2012-05-18 14:02:13] Exception: Something is wrong with the
> copy-number ratios of sample
> 'MSK_00001_251469322729,S01_CGH-v4_91__GCN_V3,log2ratio,total' relative to
> reference '
> .average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c' on chromosome
> 1. Too many non-finite values: 6721 (34.9% > 20.0%) out of 19246.
As I understand it, you're imported CN signals are already ratios,
i.e. ratios relative to a reference. When you do:
sm <- CbsModel(ds)
the CbsModel code is not clever enough to know this, so it will do use
the default and pool across all samples in 'ds' and use their average
as a reference, i.e. divide your signals with. To avoid this, there
is an (yet to become official) setting you can use as follows:
sm <- CbsModel(ds)
sm$.calculateRatios <- FALSE
See if that helps.
/Henrik
[snip]
>
> Thanks a lot for the help!
>
> Ying
>
>
>> library(aroma.core)
>> library(aroma.cn)
>> chipType <- "HG-CGH-244A,TCGA_GBM_MSK"
>> unf <- TextUnitNamesFile$byChipType(chipType)
>> ugp <- getAromaUgpFile(unf)
>> dataSet <- "TCGA_GBM_MSKCC"
>> ds <- AromaUnitTotalCnBinarySet$byName(dataSet, chipType=chipType)
>> print(ds)
> AromaUnitTotalCnBinarySet:
> Name: TCGA_GBM_MSKCC
> Tags:
> Full name: TCGA_GBM_MSKCC
> Number of files: 6
> Names: MSK_00001_251469322729, MSK_00003_251469322731,
> MSK_00006_251469322732, ..., MSK_00010_251469322627 [6]
> Path (to the first file): rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Total file size: 5.40 MB
> RAM: 0.01MB
>> sm <- CbsModel(ds)
> Loading required package: DNAcopy
>> print(sm)
> CbsModel:
> Name: TCGA_GBM_MSKCC
> Tags:
> Chip type (virtual): HG-CGH-244A
> Path: cbsData/TCGA_GBM_MSKCC/HG-CGH-244A
> Number of chip types: 1
> Sample & reference file pairs:
> Chip type #1 ('HG-CGH-244A') of 1:
> Sample data set:
> AromaUnitTotalCnBinarySet:
> Name: TCGA_GBM_MSKCC
> Tags:
> Full name: TCGA_GBM_MSKCC
> Number of files: 6
> Names: MSK_00001_251469322729, MSK_00003_251469322731,
> MSK_00006_251469322732, ..., MSK_00010_251469322627 [6]
> Path (to the first file): rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Total file size: 5.40 MB
> RAM: 0.01MB
> Reference data set/file:
> <average across arrays>
> RAM: 0.00MB
>> fit(sm, verbose=-10)
> Building tuple of reference sets...
> No reference available.
> Calculating average copy-number signals...
> Retrieving average unit signals across 6 arrays...
> Searching for an existing file...
> Paths:
> [1] "rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK"
> Filename:
> .average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c.asb
> Searching path #1 of 1...
> Path: rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Pathname:
> rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK/.average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c.asb
> Found an existing file.
> Searching path #1 of 1...done
> Located pathname:
> rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK/.average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c.asb
> Searching for an existing file...done
> Loading existing data file...
> Loading existing data file...done
> AromaUnitTotalCnBinaryFile:
> Name: .average-signals-median-mad
> Tags: 78c9a8b043bc37fd29db00f3f674295c
> Full name: .average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c
> Pathname:
> rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK/.average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c.asb
> File size: 921.57 kB (943689 bytes)
> RAM: 0.00 MB
> Number of data rows: 235834
> File format: v1
> Dimensions: 235834x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120518 13:04:05
> EDT</createdOn><platform>Agilent</platform><chipType>HG-CGH-244A</chipType><srcDetails><nbrOfFiles>6</nbrOfFiles><checkSum>5629a7bc8e75693ad556a0d8c9f3417c</checkSum></srcDetails><params><meanName>median</meanName><sdName>mad</sdName></params>
> Platform: Agilent
> Chip type: HG-CGH-244A
> Number of units to be updated: 7
> Processing chunk...
> chr "Indices in chunk:"
> int [1:7] 93672 120223 160149 216186 234895 234902 234936
> Reading data...
> Reading data...done
> Estimating averages and standard deviations...
> Estimating averages and standard deviations...done
> Writing estimates...
> Writing estimates...done
> Processing chunk...done
> Retrieving average unit signals across 6 arrays...done
> Calculating average copy-number signals...done
> Building tuple of reference sets...done
> Using reference tuple:
> AromaUnitTotalCnBinarySetTuple:
> Name: TCGA_GBM_MSKCC
> Tags:
> Chip types: HG-CGH-244A
> AromaUnitTotalCnBinarySet:
> Name: TCGA_GBM_MSKCC
> Tags:
> Full name: TCGA_GBM_MSKCC
> Number of files: 6
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [6]
> Path (to the first file): rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Total file size: 5.40 MB
> RAM: 0.01MB
> RAM: 0.00MB
> Extract DataFileMatrix...
> Array: 1
> Test data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: TCGA_GBM_MSKCC
> Tags:
> Chip types: HG-CGH-244A
> AromaUnitTotalCnBinarySet:
> Name: TCGA_GBM_MSKCC
> Tags:
> Full name: TCGA_GBM_MSKCC
> Number of files: 6
> Names: MSK_00001_251469322729, MSK_00003_251469322731,
> MSK_00006_251469322732, ..., MSK_00010_251469322627 [6]
> Path (to the first file): rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Total file size: 5.40 MB
> RAM: 0.01MB
> RAM: 0.00MB
> Reference data sets:
> AromaUnitTotalCnBinarySetTuple:
> Name: TCGA_GBM_MSKCC
> Tags:
> Chip types: HG-CGH-244A
> AromaUnitTotalCnBinarySet:
> Name: TCGA_GBM_MSKCC
> Tags:
> Full name: TCGA_GBM_MSKCC
> Number of files: 6
> Names: .average-signals-median-mad, .average-signals-median-mad,
> .average-signals-median-mad, ..., .average-signals-median-mad [6]
> Path (to the first file): rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK
> Total file size: 5.40 MB
> RAM: 0.01MB
> RAM: 0.00MB
> Test data files:
> $`HG-CGH-244A`
> AromaUnitTotalCnBinaryFile:
> Name: MSK_00001_251469322729
> Tags: S01_CGH-v4_91__GCN_V3,log2ratio,total
> Full name: MSK_00001_251469322729,S01_CGH-v4_91__GCN_V3,log2ratio,total
> Pathname:
> rawCnData/TCGA_GBM_MSKCC/HG-CGH-244A,TCGA_GBM_MSK/MSK_00001_251469322729,S01_CGH-v4_91__GCN_V3,log2ratio,total.asb
> File size: 921.40 kB (943513 bytes)
> RAM: 0.00 MB
> Number of data rows: 235834
> File format: v1
> Dimensions: 235834x1
> Column classes: double
> Number of bytes per column: 4
> Footer: <createdOn>20120518 11:04:29
> EDT</createdOn><platform>Agilent</platform><chipType>HG-CGH-244A</chipType>
> Platform: Agilent
> Chip type: HG-CGH-244A
>
> attr(,"class")
> [1] "AromaUnitTotalCnBinaryFileList" "GenericDataFileList"
> "list"
> Extract DataFileMatrix...done
> Genomic-signal tags: S01_CGH-v4_91__GCN_V3,log2ratio,total
> Reference tags: 216b0999d2e57831383f208942c5d3c6
> Array #1 ('MSK_00001_251469322729') of 6 on chromosome 1...
> Error in getRawCnData.CopyNumberChromosomalModel(this, ceList = ceList, :
>
> [2012-05-18 14:02:13] Exception: Something is wrong with the copy-number
> ratios of sample
> 'MSK_00001_251469322729,S01_CGH-v4_91__GCN_V3,log2ratio,total' relative to
> reference '.average-signals-median-mad,78c9a8b043bc37fd29db00f3f674295c' on
> chromosome 1. Too many non-finite values: 6721 (34.9% > 20.0%) out of 19246.
> at #06. getRawCnData.CopyNumberChromosomalModel(this, ceList = ceList,
> refList = rfList, chromosome = chromosome, ..., estimateSd =
> FALSE,
> verbose = less(verbose))
> - getRawCnData.CopyNumberChromosomalModel() is in environment
> 'aroma.core'
> at #05. getRawCnData(this, ceList = ceList, refList = rfList, chromosome =
> chromosome,
> ..., estimateSd = FALSE, verbose = less(verbose))
> - getRawCnData() is in environment 'aroma.core'
> at #04. extractRawCopyNumbers.CopyNumberChromosomalModel(this, array =
> array,
> chromosome = chr, maxNAFraction = maxNAFraction)
> - extractRawCopyNumbe
> In addition: Warning messages:
> 1: In log(M, base = 2) : NaNs produced
> 2: In log(A, base = 2) : NaNs produced
> Array #1 ('MSK_00001_251469322729') of 6 on chromosome 1...done
>>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252 LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> States.1252
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] aroma.cn_1.0.0 DNAcopy_1.30.0 aroma.affymetrix_2.5.0
> affxparser_1.28.0 aroma.apd_0.2.2
> [6] R.huge_0.3.0 aroma.core_2.5.0 aroma.light_1.24.0
> matrixStats_0.5.0 R.rsp_0.7.5
> [11] R.cache_0.6.2 R.filesets_1.1.5 digest_0.5.2
> R.utils_1.12.1 R.oo_1.9.3
> [16] R.methodsS3_1.2.2
>>
>
> --
> 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.
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