Sorry, everyone, I was looking at the wrong directory, but I'm still waiting for the regions.xls file which summarizes all the copy number information, I didn't expect it taking so long , since all the results is ready(.png file).
Many thanks yan -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Yan Jiao Sent: 30 November 2010 13:43 To: aroma-affymetrix@googlegroups.com Subject: RE: [aroma.affymetrix] DNA segmentation result Hi Something strange on my machine, I was running the copy number segmentation, I'm at the stage: process(ce.all,chromosomes=c(8,17),verbose=TRUE) The computer has been running for almost a day, I got 604 samples, earlier when I check the CBS folder, I found all the .png file has been done, but no regions.xls file which summarize all the copy number information, but now when I check the folder, all the .png file has gone missing, the CBS folder got nothing inside, and R is still running (ce.all,chromosomes=c(8,17),verbose=TRUE)... What is happening? Before I ran this 604 samples, I did have a trial run, which only include 3 samples and it's ok, I'm not sure whether I should continue waiting for the code to finish running, or I should kill it and rerun it? If I need to rerun it, do I need to delete all the folders? Many thanks yan -----Original Message----- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Pierre Neuvial Sent: 29 November 2010 22:23 To: aroma-affymetrix@googlegroups.com Subject: Re: [aroma.affymetrix] DNA segmentation result Hi, Sure, it will be quicker. In this case, you only have to setup the CBS segmentation model, and fit it. For example: ## define the segmentation model ## (and its parameters) seg <- CbsModel(ds, min.width=5); ## perform the segmentation ## (possibly for a subset of arrays and chromosomes) fit(seg, array=2, chromosome=5, verbose=TRUE); There are other examples on the aroma project website, e.g. http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis Best, Pierre On Mon, Nov 29, 2010 at 7:33 PM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > 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/ >>>> >>>>>>>> >>>> >>>>>>> >>>> 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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 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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/
