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> http://aroma-project.org/node/43 <http://aroma-project.org/node/43 and><http://aroma-project.org/node/43 and> 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. I also have one more question regarding CBS. Once I finish CBS computing, I end up with a text file such as: sample chromosome start stop mean count 1 NA06991 1 61736 106013377 -0.002 65870 2 NA06991 1 106019206 106022376 -1.675 1 3 NA06991 1 106024056 149036525 -0.002 11462 4 NA06991 1 149040066 149256692 -0.443 141 5 NA06991 1 149259417 149436843 -0.144 36 Is there a way to map the original probe ID or gene IDs to segmentation result? I want to end up with a table that has a column for original probe ID, a column for the related CN ratio mean from CBS, a column for chromosome, and a column for chromosome start position. 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 >
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