Hi, what Pierre suggest will run the segmentation algorithm and store the results. In order to extract the segmentation results in a tabular format, you can use getRegions() on the segmentation model object, e.g.
seg <- CbsModel(ds, min.width=5); fit(seg, verbose=TRUE); df <- getRegions(seg, verbose=TRUE); The default is to return named list where each element is a data frame containing the segmentation results for a particular sample, e.g. > str(df) List of 3 $ GSM226868:'data.frame': 65 obs. of 6 variables: ..$ chromosome: int [1:65] 1 1 1 2 2 2 2 2 3 3 ... ..$ start : num [1:65] 3.09e+06 7.35e+06 3.10e+0.. ..$ stop : num [1:65] 6.87e+06 3.09e+07 2.47e+0.. ..$ mean : num [1:65] -0.3595 -0.1588 0.0803 -0.. ..$ count : int [1:65] 8 66 707 478 7 7 332 19 3.. ..$ url : Factor w/ 65 levels "http://genome.u.. $ GSM226869:'data.frame': 47 obs. of 6 variables: ..$ chromosome: int [1:47] 1 1 1 2 2 2 3 3 4 4 ... ..$ start : num [1:47] 3.09e+06 3.10e+07 1.51e+0.. ..$ stop : num [1:47] 3.09e+07 1.51e+08 2.47e+0.. ..$ mean : num [1:47] 0.0834 -0.0346 0.1096 -0... ..$ count : int [1:47] 74 355 352 358 466 19 363.. ..$ url : Factor w/ 47 levels "http://genome.u.. $ GSM226871:'data.frame': 48 obs. of 6 variables: ..$ chromosome: int [1:48] 1 1 1 2 2 3 3 4 4 4 ... ..$ start : num [1:48] 3.09e+06 1.40e+07 1.51e+0.. ..$ stop : num [1:48] 1.39e+07 1.51e+08 2.47e+0.. ..$ mean : num [1:48] 0.3212 -0.0538 -0.3136 0... ..$ count : int [1:48] 17 409 355 354 489 347 36.. ..$ url : Factor w/ 48 levels "http://genome.u.. To stack, just do: df2 <- Reduce(rbind, df); There is also writeRegions(), which writes a file to directory getPath(seg), e.g. pathname <- writeRegions(seg, verbose=-10); print(pathname); [1] "cbsData/GSE8605,ACC,-XY,BPN,-XY,AVG,A+B,FLN,-XY/Mapping10K_Xba142/GSE8605,A CC,-XY,BPN,-XY,AVG,A+B,FLN,-XY,regions.xls" That file has the same content as the one automatically generated when use process() on ChromosomeExplorer. Hope this helps (next time) /Henrik On Mon, Nov 29, 2010 at 2:23 PM, Pierre Neuvial <pie...@stat.berkeley.edu> wrote: > 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. 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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/
