Hi, Sorry to bother you again
If I don't need the chromosome Explorer as result, I just need that excel file with copy number in (regions.xls, in CBS folder), how should I set the parameter, I guess it will speed up the procedure as well, right? Many thanks yan -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: 28 November 2010 22:57 To: aroma-affymetrix Subject: Re: [aroma.affymetrix] DNAcopy parameter On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial <pie...@stat.berkeley.edu> wrote: > Hi, > > The parameters used are the default parameters of the 'segment' > function of the DNAcopy package. If you search for 'DNAcopy > parameters' on the "Search forum" box at http://aroma-project.org, you > will find this recent thread which gives an example of how these > parameters can be changed: > > http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff Note that I just posted a follow up on that thread clarified that it is now possible to specify optional arguments specific to DNAcopy::segment() as: seg <- CbsModel(ds, min.width=5); In order to find out which they are and what they do, see the specific segmentation method, i.e. help("segment", package="DNAcopy"). /Henrik > > Hope this helps. > > Pierre > > On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >> Thanks Henrik, >> I will update my R and aroma package, >> Another question is what kind of parameters of aroma use for copy number >> segmentation, if using DNAcopy as the algorithm? >> >> Many thanks >> >> yan >> >> -----Original Message----- >> From: aroma-affymetrix@googlegroups.com >> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >> Sent: 24 November 2010 17:06 >> To: aroma-affymetrix >> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >> >> Ok, after seing your sessionInfo(); >> >> You need to update to R v2.12.0, especially since you're on Windows >> 64-bit. Lots of work have been done by R core people to support >> Windows 64-bit on R v2.12.0 and beyond. There is no shortcut to this. >> >> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install >> >> Also, the Cairo package is not available for the 64-bit version of R >> on Windows. If you try install.packages("Cairo") on your Windows >> machine, CRAN should report that package is not available. Either >> you have installed it by other means or it incorrectly installed on R >> v2.11.0. >> >> /Henrik >> >> >> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> Hi Henrik, >>> >>> I did what you suggested: >>> >>>> traceback() >>> >>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'", >>> >>> pkgname, r_arch), call. = FALSE, domain = NA) >>> >>> 12: testRversion(pkgInfo, package, pkgpath) >>> >>> 11: library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical.return = TRUE, >>> >>> warn.conflicts = warn.conflicts, keep.source = keep.source) >>> >>> 10: base::require(...) >>> >>> 9: require("Cairo") >>> >>> 8: findPngDevice.default(transparent = FALSE) >>> >>> 7: findPngDevice(transparent = FALSE) >>> >>> 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.all, verbose = TRUE) >>> >>> 1: process(ce.all, verbose = TRUE) >>> >>>> sessionInfo() >>> >>> R version 2.11.0 (2010-04-22) >>> >>> x86_64-pc-mingw32 >>> >>> locale: >>> >>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United >>> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 >>> LC_NUMERIC=C >>> >>> [5] LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> >>> [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0 >>> sfit_0.1.9 aroma.affymetrix_1.7.0 aroma.apd_0.1.7 >>> affxparser_1.20.0 >>> >>> [8] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1 >>> matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0 >>> R.filesets_0.9.0 >>> >>> [15] digest_0.4.2 R.utils_1.5.3 R.oo_1.7.4 >>> R.methodsS3_1.2.1 >>> >>> loaded via a namespace (and not attached): >>> >>> [1] tools_2.11.0 >>> >>>> >>> >>> process(ce,chromosomes=c(1,8,17), verbose=-10) >>> >>> Generating ChromosomeExplorer report... >>> >>> Setting up ChromosomeExplorer report files... >>> >>> Copying template files... >>> >>> Source path: >>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes >>> >>> Destination path: reports/includes >>> >>> Copying template files...done >>> >>> Setting up ChromosomeExplorer report files...done >>> >>> Explorer output version: 3 >>> >>> Compiling ChromosomeExplorer.onLoad.js.rsp... >>> >>> Source: >>> >>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp >>> >>> Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY >>> >>> Scanning directories for available chip types... >>> >>> Detected chip types: Mapping50K_Hind240 >>> >>> Scanning directories for available chip types...done >>> >>> Scanning image files for available zooms... >>> >>> Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64 >>> >>> Scanning image files for available zooms...done >>> >>> Scanning directory for subdirectories... >>> >>> Detected (or default) sets: cbs >>> >>> Scanning directory for subdirectories...done >>> >>> Compiling RSP... >>> >>> member data.class dimension objectSize >>> >>> 1 chipTypes character 1 120 >>> >>> 2 chrLayers character 0 40 >>> >>> 3 sampleLabels character 3 240 >>> >>> 4 sampleLayers character 0 40 >>> >>> 5 samples character 3 240 >>> >>> 6 sets character 1 96 >>> >>> 7 zooms numeric 7 72 >>> >>> Sample names: >>> >>> [1] "GSM255038" "GSM255039" "GSM255040" >>> >>> Full sample names: >>> >>> [1] "GSM255038,total" "GSM255039,total" "GSM255040,total" >>> >>> Compiling RSP...done >>> >>> Compiling ChromosomeExplorer.onLoad.js.rsp...done >>> >>> Loading required package: Cairo >>> >>> Error: package 'Cairo' is not installed for 'arch=x64' >>> >>> Generating ChromosomeExplorer report...done >>> >>> >>> -----Original Message----- >>> From: aroma-affymetrix@googlegroups.com >>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >>> Sent: 24 November 2010 16:50 >>> To: aroma-affymetrix >>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >>> >>> Hi. >>> >>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> >>>> Hi Henrik, >>> >>>> >>> >>>> Another question, I was trying to only do segmentation on 3 chromosomes, >>>> how should I do it, I tried: >>> >>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE); >>> >>>> >>> >>>> but got error message: >>> >>>> >>> >>>> Generating ChromosomeExplorer report... >>> >>>> Loading required package: Cairo >>> >>>> Error: package 'Cairo' is not installed for 'arch=x64' >>> >>>> Generating ChromosomeExplorer report...done >>> >>> Odd, because specifying a subset of chromosomes shouldn't be any >>> >>> different from running all, as you did before. >>> >>> So, there seem to be several packages that install on R 64-bit in >>> >>> Windows, but when trying to use then fails. The Cairo package is >>> >>> actually "deprecated" (replaced with similar function builtin in R), >>> >>> but we've kept support for backward compatibilities. It seems like >>> >>> you're facing these issues - and not that many people are running >>> >>> 64-bit Windows yet so you seem to be the one hitting the bumps. >>> >>> What does traceback() give when you get the error? >>> >>> What is your sessionInfo()? >>> >>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to >>> >>> narrow down where the error occurs. >>> >>> /Henrik >>> >>>> >>> >>>> >>> >>>> Many thanks >>> >>>> >>> >>>> yan >>> >>>> >>> >>>> >>> >>>> >>> >>>> -----Original Message----- >>> >>>> From: aroma-affymetrix@googlegroups.com >>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson >>> >>>> Sent: 24 November 2010 15:08 >>> >>>> To: aroma-affymetrix >>> >>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >>> >>>> >>> >>>> Hi, >>> >>>> >>> >>>> great. Contrary to error messages, warnings are alright to get. >>> >>>> >>> >>>> /H >>> >>>> >>> >>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> >>>>> Thank you Henrik, >>> >>>>> It works now, but I got some warning: >>> >>>>> >>> >>>>> process(ce, verbose=TRUE); >>> >>>>> Generating ChromosomeExplorer report... >>> >>>>> Loading required package: Cairo >>> >>>>> Generating ChromosomeExplorer report...done >>> >>>>> [1] TRUE >>> >>>>> Warning messages: >>> >>>>> 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/gs, >>>>> /gs, C:\Program Files\Common Files/gs >>> >>>>> >>> >>>>> Are those warning messages serious? Could I ignore them? >>> >>>>> >>> >>>>> >>> >>>>> Yan >>> >>>>> >>> >>>>> -----Original Message----- >>> >>>>> From: aroma-affymetrix@googlegroups.com >>>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik >>>>> Bengtsson >>> >>>>> Sent: 23 November 2010 21:53 >>> >>>>> To: aroma-affymetrix >>> >>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >>> >>>>> >>> >>>>> Hi. >>> >>>>> >>> >>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> >>>>>> Hi Henrik, >>> >>>>>> >>> >>>>>> Sorry, the error is after >>> >>>>>> cbs <- CbsModel(ds); >>> >>>>>> ce <- ChromosomeExplorer(cbs); >>> >>>>>> process(ce, verbose=TRUE); >>> >>>>> >>> >>>>> Ok, now the error message makes a bit more sense (it was my suspicion >>> >>>>> but I didn't want make guesses). >>> >>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Generating ChromosomeExplorer report... >>> >>>>>> Loading required package: Cairo >>> >>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): >>>>>> unable >>> >>>>>> to load shared library >>> >>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll': >>> >>>>>> LoadLibrary failure: The specified module could not be found. >>> >>>>>> >>> >>>>>> And there is a pop out window saying: The program can't start because >>> >>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the >>>>>> program >>> >>>>>> to fix this program. >>> >>>>> >>> >>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if >>> >>>>> you try library("GLAD"). It is because we utilize part of the GLAD >>> >>>>> package, if and only if it is *installed*, and otherwise we turn to >>> >>>>> backup solutions. What happens here is that *GLAD is installed but >>> >>>>> doesn't load*, which causes the error so that backup solutions doesn't >>> >>>>> kick in. In the next release I'll try to make sure the backup >>> >>>>> solutions will also work when there is an error load GLAD. In >>> >>>>> meanwhile, you can do this: >>> >>>>> >>> >>>>> WORKAROUND: >>> >>>>> >>> >>>>> 1. Uninstall the GLAD package (it doesn't work anyway): >>> >>>>> >>> >>>>>> remove.packages("GLAD") >>> >>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12' >>> >>>>> (as 'lib' is unspecified) >>> >>>>> >>> >>>>>> library("GLAD") >>> >>>>> Error in library("GLAD") : there is no package called 'GLAD' >>> >>>>> >>> >>>>> That should do it. Let me know if it works for you. >>> >>>>> >>> >>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL) >>> >>>>> is not installed on the system (hence the 'gsl' part of >>> >>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in >>> >>>>> order to use the GLAD package, cf. >>> >>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html. There >>> >>>>> exist 32-bit binaries of GSL at >>> >>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm. Unfortunately, it >>> >>>>> does not work for the 64-bit version of R on Windows 64-bit. It works >>> >>>>> if you do tricks an run the 32-bit version of R, but that is a rather >>> >>>>> inconvenient workaround. >>> >>>>> >>> >>>>> /Henrik >>> >>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Yan >>> >>>>>> >>> >>>>>> -----Original Message----- >>> >>>>>> From: aroma-affymetrix@googlegroups.com >>> >>>>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik >>>>>> Bengtsson >>> >>>>>> Sent: 23 November 2010 18:50 >>> >>>>>> To: aroma-affymetrix >>> >>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error >>> >>>>>> >>> >>>>>> Hi. >>> >>>>>> >>> >>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> Dear all, >>> >>>>>>> >>> >>>>>>> I'm trying to do DNA segmentation, >>> >>>>>>> >>> >>>>>>> This is what I'm doing: >>> >>>>>>> >>> >>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", >>> >>>>>> verbose=TRUE); >>> >>>>>>> >>> >>>>>>> ###this is done sucessfully >>> >>>>>>> >>> >>>>>>> # Segmentation >>> >>>>>>> >>> >>>>>>> cbs <- CbsModel(ds); >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm >>> >>>>>> trying >>> >>>>>>> to use DNAcopy for segmentation. >>> >>>>>> >>> >>>>>> Is it really the case that you get that error when you do: >>> >>>>>> >>> >>>>>> cbs <- CbsModel(ds); >>> >>>>>> >>> >>>>>> or do you do anything else? Is suspect you do something more. >>> >>>>>> >>> >>>>>> Also, after you got the error, could you cut'n'paste the verbose >>> >>>>>> output including any error messages you get and send it to us? Also, >>> >>>>>> make sure to report what print(traceback()) gives immediate after >>> >>>>>> getting the error. >>> >>>>>> >>> >>>>>> /Henrik >>> >>>>>> >>> >>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation >>> >>>>>> method because it contains information about cytobands. >>> >>>>>> >>> >>>>>>> >>> >>>>>>> How to change it? >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> Many thanks >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> yan >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>>>>>> ********************************************************************** >>> >>>>>>> >>> >>>>>>> This email and any files transmitted with it are confidential and >>> >>>>>>> >>> >>>>>>> intended solely for the use of the individual or entity to whom they >>> >>>>>>> >>> >>>>>>> are addressed. If you have received this email in error please notify >>> >>>>>>> >>> >>>>>>> the system manager (it.supp...@cancer.ucl.ac.uk). >>> >>>>>>> >>> >>>>>>> >>>>>>> ********************************************************************** >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> -- >>> >>>>>>> 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 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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/ >>> >>>> >>> >>>> -- >>> >>>> 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/ >>> >>> -- >>> 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/ >> >> -- >> 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/ > -- 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/
