Hi.
On Fri, Mar 11, 2011 at 2:53 AM, mortiz <mortiz...@gmail.com> wrote:
> hi everyone,
>
> i still have some problems with this.
So time's fly; you're version of aroma.affymetrix is yet again
outdated, so you need to updated in order to the correct
troubleshooting (the problem may not be there in the new version or
you may get a more informative error message).
> 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$getIndex(idx, max = n)
> at getFile.GenericDataFileSet(this, 1)
> at getFile(this, 1)
> at getUnitNamesFile.AffymetrixCelSet(this)
> at getUnitNamesFile(this)
> at getChipType.AffymetrixCelSet(X[[1]], ...)
> at FUN(X[[1]], ...)
> at lapply(X, FUN, ...)
> at sapply.default(res, FUN = getChipType)
> at sapply(res, FUN = getChipType)
> at getSets.AromaMicroarrayDataSetTuple(this)
> at getSets(this)
I *guess* this is because the data sets for the two chip type use
different *names* for the same samples. Basically, if you compare:
getNames(cesNList[[1]])
getNames(cesNList[[2]])
they are not matching. Hint: the names contain "(Mapping250K_Nsp)"
and "(Mapping250K_Sty)". You can use so called fullnames translators
to fix this, cf. How-to page 'Use fullname translators to rename data
files':
http://aroma-project.org/howtos/setFullNamesTranslator
Do it on each of two sets in 'cesNList'.
Let's see if that helps/makes a difference.
/Henrik
>
> Además: Mensajes de aviso perdidos
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE, :
> there is no package called 'Cairo'
> 2: In method(static, ...) :
> Ghostscript not found. Searched directories: C:/gs, C:\Program Files
> (x86)/gs, /gs, C:\Program Files (x86)\Common Files/gs
> 20110311 11:47:55|Generating ChromosomeExplorer report...done
>
>
>> traceback()
> 45: throw.Exception(Exception(...))
> 44: throw(Exception(...))
> 43: throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s,%s]) implies that is should be empty.",
> length(x), range[1], range[2]))
> 42: throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) implies that is should be empty.",
> length(x), range[1], range[2]))
> 41: getIndices.Arguments(static, ..., length = length)
> 40: getIndices(static, ..., length = length)
> 39: method(static, ...)
> 38: Arguments$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/
>
--
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/
