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
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