Hi.
On Mon, Mar 28, 2011 at 3:06 AM, mortiz <mortiz...@gmail.com> wrote:
> hi,
>
> I have two problems now. One is that im working with 105 arrays and
> when i try to do ChromosomeExplorer it reachs
>
>> ce <- ChromosomeExplorer(cbs)
>> process(ce, verbose=verbose, zooms=c(4))
> 20110328 11:58:40|Generating ChromosomeExplorer report...
> 20110328 11:58:40| Setting up ChromosomeExplorer report files...
> 20110328 11:58:40| Copying template files...
> 20110328 11:58:40| Source path: C:/PROGRA~1/R/R-212~1.1/library/
> aroma.core/reports/includes
> 20110328 11:58:40| Destination path: reports/includes
> 20110328 11:58:43| Copying template files...done
> 20110328 11:58:43| Setting up ChromosomeExplorer report files...done
> 20110328 11:58:43| Copying ChromosomeExplorer.html...
> 20110328 11:58:43| Source pathname: C:/PROGRA~1/R/R-212~1.1/library/
> aroma.core/reports/templates/html/ChromosomeExplorer/
> ChromosomeExplorer.html
> 20110328 11:58:43| Destination pathname: reports/CELLungCIMA/ACC,-
> XY,QN,BPN,-XY,NMF,refs,FLN,-XY,SA,alpha+sdundo/ChromosomeExplorer.html
> 20110328 11:58:43| Copying ChromosomeExplorer.html...done
> 20110328 11:58:43| Explorer output version: 3
> 20110328 11:58:44| Compiling ChromosomeExplorer.onLoad.js.rsp...
> 20110328 11:58:44| Source: C:/PROGRA~1/R/R-212~1.1/library/aroma.core/
> reports/templates/rsp/ChromosomeExplorer3/
> ChromosomeExplorer.onLoad.js.rsp
> 20110328 11:58:44| Output path: reports/CELLungCIMA/ACC,-XY,QN,BPN,-
> XY,NMF,refs,FLN,-XY,SA,alpha+sdundo
> 20110328 11:58:44| Scanning directories for available chip types...
> 20110328 11:58:44| Detected chip types: Mapping250K_Nsp+Sty
> 20110328 11:58:44| Scanning directories for available chip
> types...done
> 20110328 11:58:44| Scanning image files for available zooms...
> 20110328 11:58:44| Detected (or default) zooms: 1, 2, 4, 8, 16, 32,
> 64
> 20110328 11:58:44| Scanning image files for available zooms...done
> 20110328 11:58:44| Scanning directory for subdirectories...
> 20110328 11:58:44| Detected (or default) sets: cbs
> 20110328 11:58:44| Scanning directory for subdirectories...done
> 20110328 11:58:44| Compiling RSP...
>
> and it stays there forever (i mean 4 days in a row without doing
> anythingelse...)
Hmm... so, internally the fullnames translator function is used, so if
you wrote a very inefficient one, it may be the cause (but 4 days
sounds crazy). What does your fullnames translator look like?
Also, try this:
tuple <- getSetTuple(cbs);
print(tuple);
fullnames <- getFullNames(tuple, arrays=1);
str(fullnames);
fullnames <- getFullNames(tuple, arrays=1:10);
str(fullnames);
fullnames <- getFullNames(tuple, arrays=1:50);
str(fullnames);
fullnames <- getFullNames(tuple);
str(fullnames);
Are any of these very slow? Does it get worse when more arrays you
are querying?
>
> The second one is that ive tried now to change some cbs parameters and
> when i try to execute it now i get this error
>
>> fit(cbs, chromosomes=c(1))
> Error en list(`fit(cbs, chromosomes = c(1))` = <environment>,
> `fit.CopyNumberSegmentationModel(cbs, chromosomes = c(1))` =
> <environment>, :
>
> [2011-03-28 11:59:24] Exception: Something is wrong with the copy-
> number ratios of sample 'BN 01 (Mapping250K),chipEffects' relative to
> reference '.average-intensities-median-mad,
> 86474737cc816d4abb8d5db99a5516e7' on chromosome 1. Too many non-finite
> values: 16887 (83.0% > 20.0%) out of 20342.
Do you get the same for other arrays, e.g.
fit(cbs, arrays=2, chromosomes=c(1))
Also, I see you run CRMA with ACNE. For troubleshooting, see if you
get the same if you run plain CRMA. If you don't, it's an issue for
convergence for ACNE. If you do still have an error, it is likely
something with the same data.
/Henrik
> at throw(Exception(...))
> at throw.default(sprintf("Something is wrong with the copy-number
> ratios of sample '%s' relative to reference '%s' on chromosome %s. Too
> many non-finite values: %d (%.1f%% >
> at throw(sprintf("Something is wrong with the copy-number ratios of
> sample '%s' relative to reference '%s' on chromosome %s. Too many non-
> finite values: %d (%.1f%% > %.1f%%)
> at getRawCnData.CopyNumberChromosomalModel(this, ceList = ceList,
> refList = rfList, chromosome = chromosome, ..., estimateSd = FALSE,
> verbose = less(verbose))
> at getRawCnData(this, ceList = ceList, refList = rfList, chromosome
> = chromosome, ..., estimateSd = FALSE, verbose = less(verbose))
> at extractRawCopy
>
>> 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), BN 02 (Mapping250K), ..., VB95
> (Mapping250K)
> 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), BN 02 (Mapping250K), ..., VB95
> (Mapping250K)
> Time period: 2011-03-28 10:49:55 -- 2011-03-28 10:50:28
> Total file size: 913.33MB
> RAM: 0.12MB
> Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
> combineAlleles: logi TRUE)
>
>> 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
> LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] DNAcopy_1.24.0 ACNE_0.4.2
> MASS_7.3-9 aroma.affymetrix_2.0.0 aroma.apd_0.1.8
> affxparser_1.22.1 R.huge_0.2.2
> [8] aroma.core_2.0.0 aroma.light_1.18.3
> matrixStats_0.2.2 R.rsp_0.4.5 R.cache_0.4.0
> R.filesets_0.9.5 digest_0.4.2
> [15] R.utils_1.6.5 R.oo_1.7.5
> R.methodsS3_1.2.1
>>
>
> On 14 mar, 06:26, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> 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
>>
>> ...
>>
>> leer más »
>
> --
> 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
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> 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/
