Hi Hendrik,
it works now without error messages! Thanks!
The chromosome explorer looks fine except for chromosomes > 19. There
are links for chromosomes 20,21,22 and X in the navigation bar that do
not work (since mice do not have chr. 20,21,22). Y and M are not
linked. I read in this forum that the links currently are "hard
coded". However, this is not a big problem for me.
Thanks,
Hans-Ulrich
On Dec 8, 1:37 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> it looks like the patch wasn't applied. I've actually committed the
> bug fix to CRAN where aroma.core v1.8.1 is now available. If you do
>
> source("http://aroma-project.org/hbLite.R";);
> hbInstall("aroma.affymetrix");
>
> that one should install (and any patches will be dropped).
>
> Let me know if you still have problems
>
> /Henrik
>
> On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich
>
> <hans-ulrich.kl...@uni-muenster.de> wrote:
> > Hi Hendrik,
>
> > I installed the patches and removed the report and the cbs folder.
> > Then, I run the segmentation and the chromosome explorer again. I got
> > the same/similar error message (see below). The error occured when
> > processing the second sample so the first one seems to run without
> > problems.
> > Can I run the chromosome explorer and exclude chromosome 25?
>
> > Regards,
> > Hans-Ulrich
>
> > 20101206 12:53:52| Plotting S2 for chromosome 24 [NAMB]...done
> > 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
> > hooks...done
> > 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 24...done
> > 20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 25...
> > 20101206 12:53:52| Loading results from file...
> > 20101206 12:53:52| Pathname: cbsData/Koschmieder,ACC,ra,-XY,BPN,-
> > XY,RMA,A+B,FLN,-XY,paired/MOUSEDIVm520650/
> > S2,chr25,9012c8079b8a75fe8fc388ca02bfb65e.xdr
> > 20101206 12:53:52| Fit object: DNAcopy
> > 20101206 12:53:52| Loading results from file...done
> > 20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
> > hooks...
> > ERROR caught in onFit.CopyNumberSegmentationModel():
> > [2010-12-06 12:53:53] Exception: Cannot infer number of bases in
> > chromosome. No such chromosome: 25
> > at throw(Exception(...))
> > at throw.default("Cannot infer number of bases in chromosome. No
> > such chromoso
> > at throw("Cannot infer number of bases in chromosome. No such
> > chromosome: ", c
> > at getChromosomeLength(chromosome)
> > at doTryCatch(return(expr), name, parentenv, handler)
> > at tryCatchOne(expr, names, parentenv, handlers[[1]])
> > at tryCatchList(expr, classes, parentenv, handlers)
> > at tryCatch({
> > at fcn(...)
> > at doTryCatch(return(expr), name, parentenv, handler)
> > at tryCatchOne(expr, names, parentenv, handlers[[1]])
> > at tryCatchList(expr, classes, parentenv, handlers)
> > at tryCatch({
> > at callHooks.list(hooks, ...)
> > at callHooks(hooks, ...)
> > at callHooks.default(hookName, fit = fit, chromosome = chr, fullname
> > = fullnam
> > at callHooks(hookName, fit = fit, chromosome = chr, fullname =
> > fullname)
> > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> > verbose = v
> > at fit(this, ..., .retResults = FALSE, verbose = verbose)
> > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> > = "png", p
> > at plot(model, path = path, imageFormat = "png", plotband =
> > plotband, arrays =
> > at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
> > = chromos
> > at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
> > zooms = zooms
> > at process.ChromosomeExplorer(ce, verbose = verbose)
> > at process(ce, verbose = verbose)
> > used (Mb) gc trigger (Mb) max used (Mb)
> > Ncells 1178686 63 4079505 217.9 26615696 1421.5
> > Vcells 1568318 12 4818496 36.8 41974408 320.3
> > 20101206 12:53:53| Calling onFit.CopyNumberSegmentationModel()
> > hooks...done
> > 20101206 12:53:53|Calling onFit.CopyNumberSegmentationModel()
> > hooks...done
> > Error in list(`process(ce, verbose = verbose)` = <environment>,
> > `process.ChromosomeExplorer(ce, verbose = verbose)` =
> > <environment>, :
>
> > [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
> > makes 'indentPos' negative: -1
> > at throw(Exception(...))
> > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative:
> > at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative: ", this
> > at exit.Verbose(verbose)
> > at exit(verbose)
> > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> > verbose = v
> > at fit(this, ..., .retResults = FALSE, verbose = verbose)
> > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> > = "png", p
> > at plot(model, path = path, imageFormat = "png", plotband =
> > plotband, arrays =
> > at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
> > = chromos
> > at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
> > zooms = zooms
> > at process.ChromosomeExplorer(ce, verbose = verbose)
> > at process(ce, verbose = verbose)
> > Error in list(`process(ce, verbose = verbose)` = <environment>,
> > `process.ChromosomeExplorer(ce, verbose = verbose)` =
> > <environment>, :
>
> > [2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
> > makes 'indentPos' negative: -1
> > at throw(Exception(...))
> > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative:
> > at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative: ", this
> > at exit.Verbose(this)
> > at exit(this)
> > at popState.Verbose(verbose)
> > at popState(verbose)
> > at throw.Exception(Exception(...))
> > at throw(Exception(...))
> > at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative:
> > at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
> > negative: ", this
> > at exit.Verbose(verbose)
> > at exit(verbose)
> > at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
> > verbose = v
> > at fit(this, ..., .retResults = FALSE, verbose = verbose)
> > at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
> > = "png", p
> > at plot(model, path = path, imageFormat = "png", plotband =
> > plotband, arrays =
> > at writeGraphs.ChromosomeExplore
> > 20101206 12:53:53|Generating ChromosomeExplorer report...done
>
> > On Dec 3, 8:09 am, Henrik Bengtsson <henrik.bengts...@aroma-
> > project.org> wrote:
> >> Hi,
>
> >> I could reproduce this error (also on the Human genome when trying to
> >> generate CE plots for Chr25). It's a bug, which I have patched (until
> >> next release). Run the following and the patches will be installed
> >> too:
>
> >> source("http://aroma-project.org/hbLite.R";);
> >> hbInstall("aroma.affymetrix");
>
> >> Let me know if it solves your problem.
>
> >> /Henrik
>
> >> On Wed, Dec 1, 2010 at 2:28 PM, Hans-Ulrich
>
> >> <hans-ulrich.kl...@uni-muenster.de> wrote:
> >> > Sorry, I forgot that:
>
> >> >> sessionInfo()
> >> > R version 2.12.0 (2010-10-15)
> >> > Platform: x86_64-pc-linux-gnu (64-bit)
>
> >> > locale:
> >> > [1] C
>
> >> > attached base packages:
> >> > [1] stats graphics grDevices utils datasets methods
> >> > base
>
> >> > other attached packages:
> >> > [1] Cairo_1.4-5 RColorBrewer_1.0-2
> >> > DNAcopy_1.24.0
> >> > [4] preprocessCore_1.12.0 sfit_0.1.9
> >> > aroma.affymetrix_1.8.1
> >> > [7] aroma.apd_0.1.7 affxparser_1.22.0
> >> > R.huge_0.2.0
> >> > [10] aroma.core_1.8.0 aroma.light_1.18.2
> >> > matrixStats_0.2.2
> >> > [13] R.rsp_0.4.0 R.cache_0.3.0
> >> > R.filesets_0.9.1
> >> > [16] digest_0.4.2 R.utils_1.5.8
> >> > R.oo_1.7.4
> >> > [19] R.methodsS3_1.2.1
>
> >> > loaded via a namespace (and not attached):
> >> > [1] tools_2.12.0
> >> > Warning message:
> >> > 'DESCRIPTION' file has 'Encoding' field and re-encoding is not
> >> > possible
>
> >> > Regards,
> >> > Hans-Ulrich
>
> >> > On Dec 1, 6:44 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> >> > project.org> wrote:
> >> >> Hi,
>
> >> >> before anything else, are you running the latest aroma.affymetrix
> >> >> (v1.8.0), i.e. what's your sessionInfo()?
>
> >> >> /Henrik
>
> >> >> On Wed, Dec 1, 2010 at 9:32 AM, Hans-Ulrich
>
> >> >> <hans-ulrich.kl...@uni-muenster.de> wrote:
> >> >> > Hi Hendrik,
>
> >> >> > I created a file for the mouse genome. However, I still get an error
> >> >> > message:
>
> >> >> >> cbs = CbsModel(cesNSamples, cesNControls, genome="Mouse")
> >> >> >> df <- getGenomeData(cbs, verbose=verbose)
> >> >> > 20101201 14:44:53|Reading genome chromosome annotation file...
> >> >> > 20101201 14:44:53| Searching for the file...
> >> >> > 20101201 14:44:54| Searching for the file...done
> >> >> > 20101201 14:44:54| Reading data file...
> >> >> > 20101201 14:44:54| Pathname: annotationData/genomes/Mouse/
> >> >> > Mouse,chromosomes.txt
> >> >> > 20101201 14:44:54| Reading data file...done
> >> >> > 20101201 14:44:54| Translating chromosome names...
> >> >> > 20101201 14:44:54| Translating chromosome names...done
> >> >> > 20101201 14:44:54|Reading genome chromosome annotation file...done
> >> >> >> df
> >> >> > nbrOfBases nbrOfGenes
> >> >> > 1 197195432 1237
> >> >> > 2 181748087 1779
> >> >> > 3 159599783 1046
> >> >> > 4 155630120 1286
> >> >> > 5 152537259 1285
> >> >> > 6 149517037 1158
> >> >> > 7 152524553 1975
> >> >> > 8 131738871 1082
> >> >> > 9 124076172 1260
> >> >> > 10 129993255 1036
> >> >> > 11 121843856 1606
> >> >> > 12 121257530 712
> >> >> > 13 120284312 850
> >> >> > 14 125194864 860
> >> >> > 15 103494974 823
> >> >> > 16 98319150 679
> >> >> > 17 95272651 1075
> >> >> > 18 90772031 522
> >> >> > 19 61342430 739
> >> >> > 23 166650296 800
> >> >> > 24 15902555 12
> >> >> > M 16299 13
> >> >> >> fit(cbs, min.width=5, verbose=verbose)
> >> >> >> ce = ChromosomeExplorer(cbs)
> >> >> >> process(ce, verbose=verbose)
> >> >> > [...]
> >> >> > ERROR caught in onFit.CopyNumberSegmentationModel():
> >> >> > [2010-12-01 18:18:04] Exception: Cannot infer number of bases in
> >> >> > chromosome. No such chromosome: 25
> >> >> > at throw(Exception(...))
> >> >> > at throw.default("Cannot infer number of bases in chromosome. No
> >> >> > such chromoso
> >> >> > at throw("Cannot infer number of bases in chromosome. No such
> >> >> > chromosome: ", c
> >> >> > at getChromosomeLength(chromosome)
> >> >> > at doTryCatch(return(expr), name, parentenv,
>
> ...
>
> read more »
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