hi everyone, i still have some problems with this. Now I get an error when I execute
> cbs <- CbsModel(cesNList) > ce <- ChromosomeExplorer(cbs) > process(ce,verbose=verbose, zooms=c(4)) 20110311 11:47:55| Using reference tuple: Error en list(`process(ce, verbose = verbose, zooms = c(4))` = <environment>, : [2011-03-11 11:47:55] Exception: Argument 'x' is of length 1 although the range ([0,0]) implies that is should be empty. at throw(Exception(...)) at throw.default(sprintf("Argument 'x' is of length %d although the range ([%s,%s]) implies that is should be empty.", length(x), range[1], range[2])) at throw(sprintf("Argument 'x' is of length %d although the range ([%s,%s]) implies that is should be empty.", length(x), range[1], range[2])) at getIndices.Arguments(static, ..., length = length) at getIndices(static, ..., length = length) at method(static, ...) at Arguments$getIndex(idx, max = n) at getFile.GenericDataFileSet(this, 1) at getFile(this, 1) at getUnitNamesFile.AffymetrixCelSet(this) at getUnitNamesFile(this) at getChipType.AffymetrixCelSet(X[[1]], ...) at FUN(X[[1]], ...) at lapply(X, FUN, ...) at sapply.default(res, FUN = getChipType) at sapply(res, FUN = getChipType) at getSets.AromaMicroarrayDataSetTuple(this) at getSets(this) Además: Mensajes de aviso perdidos 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'Cairo' 2: In method(static, ...) : Ghostscript not found. Searched directories: C:/gs, C:\Program Files (x86)/gs, /gs, C:\Program Files (x86)\Common Files/gs 20110311 11:47:55|Generating ChromosomeExplorer report...done > traceback() 45: throw.Exception(Exception(...)) 44: throw(Exception(...)) 43: throw.default(sprintf("Argument 'x' is of length %d although the range ([%s,%s]) implies that is should be empty.", length(x), range[1], range[2])) 42: throw(sprintf("Argument 'x' is of length %d although the range ([%s,%s]) implies that is should be empty.", length(x), range[1], range[2])) 41: getIndices.Arguments(static, ..., length = length) 40: getIndices(static, ..., length = length) 39: method(static, ...) 38: Arguments$getIndex(idx, max = n) 37: getFile.GenericDataFileSet(this, 1) 36: getFile(this, 1) 35: getUnitNamesFile.AffymetrixCelSet(this) 34: getUnitNamesFile(this) 33: getChipType.AffymetrixCelSet(X[[1L]], ...) 32: FUN(X[[1L]], ...) 31: lapply(X, FUN, ...) 30: sapply.default(res, FUN = getChipType) 29: sapply(res, FUN = getChipType) 28: getSets.AromaMicroarrayDataSetTuple(this) 27: getSets(this) 26: getDefaultFullName.GenericDataFileSetList(this, ...) 25: getDefaultFullName(this, ...) 24: getFullName.FullNameInterface(this, ...) 23: getFullName(this, ...) 22: getName.FullNameInterface(this) 21: getName(this) 20: paste("Name:", getName(this)) 19: as.character.AromaMicroarrayDataSetTuple(x) 18: as.character(x) 17: print(as.character(x)) 16: print.Object(...) 15: print(...) 14: eval.with.vis(expr, pf, NULL) 13: evalVis(expr) 12: capture.Verbose(this, print(...), level = level) 11: capture(this, print(...), level = level) 10: print.Verbose(verbose, refTuple) 9: print(verbose, refTuple) 8: fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE, verbose = verbose) 7: fit(this, ..., .retResults = FALSE, verbose = verbose) 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png", plotband = plotband, arrays = arrays, ...) 5: plot(model, path = path, imageFormat = "png", plotband = plotband, arrays = arrays, ...) 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes = chromosomes, zooms = zooms, ..., verbose = less(verbose)) 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes, zooms = zooms, ..., verbose = less(verbose)) 2: process.ChromosomeExplorer(ce, verbose = verbose, zooms = c(4)) 1: process(ce, verbose = verbose, zooms = c(4)) > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RColorBrewer_1.0-2 DNAcopy_1.24.0 ACNE_0.4.2 MASS_7.3-9 aroma.affymetrix_1.9.0 aroma.apd_0.1.8 [7] affxparser_1.22.1 R.huge_0.2.2 aroma.core_1.9.1 aroma.light_1.18.3 matrixStats_0.2.2 R.rsp_0.4.2 [13] R.cache_0.4.0 R.filesets_0.9.2 digest_0.4.2 R.utils_1.6.2 R.oo_1.7.5 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] splines_2.12.1 the variables im using are > cbs CbsModel: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Chip type (virtual): Mapping250K_Nsp+Sty Path: cbsData/CELLungCIMA,ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Nsp+Sty Number of chip types: 2 Sample & reference file pairs: Chip type #1 of 2 ('Mapping250K_Nsp'): Sample data set: CnChipEffectSet: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Path: plmData/CELLungCIMA,ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Nsp Platform: Affymetrix Chip type: Mapping250K_Nsp,monocell Number of arrays: 105 Names: BN 01 (Mapping250K_Nsp), BN 02 (Mapping250K_Nsp), ..., VB95 (Mapping250K_Nsp) Time period: 2011-03-11 09:34:01 -- 2011-03-11 09:34:13 Total file size: 1003.43MB RAM: 0.12MB Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: logi TRUE) Reference data set/file: <average across arrays> Chip type #2 of 2 ('Mapping250K_Sty'): Sample data set: CnChipEffectSet: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Path: plmData/CELLungCIMA,ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Sty Platform: Affymetrix Chip type: Mapping250K_Sty,monocell Number of arrays: 105 Names: BN 01 (Mapping250K_Sty), BN 02 (Mapping250K_Sty), ..., VB95 (Mapping250K_Sty) Time period: 2011-03-11 09:33:46 -- 2011-03-11 09:33:58 Total file size: 913.33MB RAM: 0.12MB Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: logi TRUE) Reference data set/file: <average across arrays> RAM: 0.00MB > ce ChromosomeExplorer: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Number of arrays: 0 Path: reports/CELLungCIMA/ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Nsp+Sty/cbs RAM: 0.00MB > cesNList $Mapping250K_Nsp CnChipEffectSet: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Path: plmData/CELLungCIMA,ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Nsp Platform: Affymetrix Chip type: Mapping250K_Nsp,monocell Number of arrays: 105 Names: BN 01 (Mapping250K_Nsp), BN 02 (Mapping250K_Nsp), ..., VB95 (Mapping250K_Nsp) Time period: 2011-03-11 09:34:01 -- 2011-03-11 09:34:13 Total file size: 1003.43MB RAM: 0.12MB Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: logi TRUE) $Mapping250K_Sty CnChipEffectSet: Name: CELLungCIMA Tags: ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA Path: plmData/CELLungCIMA,ACC,-XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA/ Mapping250K_Sty Platform: Affymetrix Chip type: Mapping250K_Sty,monocell Number of arrays: 105 Names: BN 01 (Mapping250K_Sty), BN 02 (Mapping250K_Sty), ..., VB95 (Mapping250K_Sty) Time period: 2011-03-11 09:33:46 -- 2011-03-11 09:33:58 Total file size: 913.33MB RAM: 0.12MB Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE, combineAlleles: logi TRUE) thanks!!! :) maria On 10 feb, 02:44, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > > > On Wed, Feb 9, 2011 at 12:59 PM,mortiz<mortiz...@gmail.com> wrote: > > hi everyone, > > > ive been having problems trying to analyze a group of samples of 250K > > using both (Nsp and Sty) enzymes. Ive followed the vignette in > > aroma.affymetrix, although i want to use CbsModel instead of > > GladModel. > > > here is some info: > > >> sessionInfo() > > R version 2.11.1 (2010-05-31) > > x86_64-pc-mingw32 > > > locale: > > [1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252 > > [3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C > > [5] LC_TIME=Spanish_Spain.1252 > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods > > base > > > other attached packages: > > [1] ACNE_0.4.2 NSA_0.0.1 > > DNAcopy_1.22.1 > > [4] calmate_0.6.2 MASS_7.3-6 > > aroma.affymetrix_1.7.0 > > [7] aroma.apd_0.1.7 affxparser_1.20.0 > > R.huge_0.2.0 > > [10] aroma.core_1.7.0 aroma.light_1.16.1 > > matrixStats_0.2.2 > > [13] R.rsp_0.4.0 R.cache_0.3.0 > > R.filesets_0.9.0 > > [16] digest_0.4.2 R.utils_1.5.3 > > R.oo_1.7.4 > > [19] R.methodsS3_1.2.1 > > You need to update; > > http://aroma-project.org/install > > > > > > > here is the code im executing > > >>setwd("D:/aroma") > >>library(aroma.affymetrix) > >>library(calmate) > >>library(NSA) > >>library(ACNE) > > >>verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > >>dataSet <- "CELLungCIMA" > >>chipTypes <- c("Mapping250K_Nsp", "Mapping250K_Sty") > > >>cdfs <- lapply(chipTypes, FUN=function(chipType) { > > AffymetrixCdfFile$byChipType(chipType) > > }) > > >>gis <- lapply(cdfs, getGenomeInformation) > > >>sis <- lapply(cdfs, getSnpInformation) > > >>cesNList <- list() > > >>chipType <- chipTypes[1] > > >>cdf <- AffymetrixCdfFile$byChipType(chipType) > >>cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf) > > >>cs <- extract(cs, !isDuplicated(cs)) > > >>acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2") > > >>csC <- process(acc, verbose=verbose) > > >>bpn <- BasePositionNormalization(csC, target="zero") > > >>csN <- process(bpn, verbose=verbose) > > >>plm <- NmfSnpPlm(csN, mergeStrands=TRUE) > > >>fit(plm, verbose=verbose) > > >>ces <- getChipEffectSet(plm) > >>fln <- FragmentLengthNormalization(ces) > > >>cesNList[[chipType]] <- process(fln, verbose=verbose) > > > and I do the same for the second enzyme with no errors. so finally i > > have cesNList which is > > >> cesNList > > $Mapping250K_Nsp > > SnpChipEffectSet: > > Name: CELLungCIMA > > Tags: ACC,-XY,BPN,-XY,NMF,FLN,-XY > > Path: plmData/CELLungCIMA,ACC,-XY,BPN,-XY,NMF,FLN,-XY/Mapping250K_Nsp > > Platform: Affymetrix > > Chip type: Mapping250K_Nsp,monocell > > Number of arrays: 105 > > Names: BN 01 (Mapping250K_Nsp), BN 02 (Mapping250K_Nsp), ..., VB95 > > (Mapping250K_Nsp) > > Time period: 2011-02-07 21:15:39 -- 2011-02-07 21:16:10 > > Total file size: 1003.43MB > > RAM: 0.17MB > > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE) > > > $Mapping250K_Sty > > SnpChipEffectSet: > > Name: CELLungCIMA > > Tags: ACC,-XY,BPN,-XY,NMF,FLN,-XY > > Path: plmData/CELLungCIMA,ACC,-XY,BPN,-XY,NMF,FLN,-XY/Mapping250K_Sty > > Platform: Affymetrix > > Chip type: Mapping250K_Sty,monocell > > Number of arrays: 105 > > Names: BN 01 (Mapping250K_Sty), BN 02 (Mapping250K_Sty), ..., VB95 > > (Mapping250K_Sty) > > Time period: 2011-02-07 21:20:10 -- 2011-02-07 21:20:36 > > Total file size: 913.33MB > > RAM: 0.17MB > > Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE) > > > but the when i try to do the segmentation it gives an error: (in the > > vignette instead of CbsModel, GladModel is used, but I guess if GLAD > > works, CBS should do it too)... > > >> cbs <- CbsModel(cesNList) > > Error en UseMethod("as.CopyNumberDataSetTuple") : > > no applicable method for 'as.CopyNumberDataSetTuple' applied to an > > object of class "c('SnpChipEffectSet', 'ChipEffectSet', > > 'ParameterCelSet', 'AffymetrixCelSet', 'AffymetrixFileSet', > > 'AromaPlatformInterface', 'AromaMicroarrayDataSet', > > 'GenericDataFileSet', 'FullNameInterface', 'Object')" > > Yes, the segmentation model classes only accept data sets that are of > class CopyNumberDataSet. A SnpChipEffectSet is not such an object, > but an CnChipEffectSet is. In addition to this, the CnChipEffectSet > must contain total CN estimates only, not allele-specific CNs (as a > SnpChipEffectSet object). This problem is completely independent of > whether you use CbsModel, GladModel or any other segmentation model. > So, in your case, you need to obtain CopyNumberDataSet:s containing > total CN estimate. For example: > > cesSList <- lapply(cesNList, FUN=function(cesN) { > as <- AlleleSummation(cesN); > print(as); > process(as, verbose=verbose); > > }); > > FYI, this is also documented in the lab 'CRMA v2 on 10K tumor data' > [http://aroma-project.org/labsessions/]. > > Then proceed with the segmentation, e.g. > > seg <- CbsModel(cesSList); > > ... > > Hope this helps > > Henrik > > > > > does anyone knows what might be happening here?? > > > thank you very much, > > > nice day! > > > maria > > > -- > > 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 websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://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. 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/