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