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 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. 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/
