Hi Yan,
You're right: removing files manually from data folders generated by
aroma.* is not a good idea. This is can be done directly within R
using the methods provided by the package.
In your case, I think you were doing :
cbs <- CbsModel(ds);
ce <- ChromosomeExplorer(cbs);
process(ce, chromosomes=c(1,8,17), verbose=TRUE);
To run the segmentation on the first two samples, you can do
process(ce, arrays=c(1,2), chromosomes=c(1,8,17), verbose=TRUE);
If you want to specify the *names* of samples to be segmented, you can use
idxs <- indexOf(ce, sampleNames);
process(ce, arrays=idxs, chromosomes=c(1,8,17), verbose=TRUE);
where 'sampleNames' is a vector of sample names.
More generally, one can use the 'extract' method on any set of data files, e.g.
ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);
idxs <- indexOf(ce, sampleNames);
dsSub <- extract(ds, idxs);
Hope this helps.
Pierre
On Thu, Nov 25, 2010 at 3:35 PM, Yan Jiao <y.j...@ucl.ac.uk> wrote:
> Now it works after I update my R.
> Another question is can I pass the sample names as a parameter to sub select
> the samples for segmentation? instead of removing the unwanted ones from data
> folder?
>
> 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
>>
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>>
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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
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>>>>> Groups "aroma.affymetrix" group with website
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>>>>> http://www.aroma-project.org/.
>>
>>>>> To post to this group, send email to aroma-affymetrix@googlegroups.com
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>>>>> To unsubscribe and other options, go to
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>>>>>
>>
>>>>> --
>>
>>>>> 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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>>>>>
>>
>>>>
>>
>>>> --
>>
>>>> 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
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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
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>>
>>> To post to this group, send email to aroma-affymetrix@googlegroups.com
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>>
>>>
>>
>>> --
>>
>>> 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.
>>
>>>
>>
>>>
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>>>
>>
>> --
>>
>> 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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>>
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>> --
>> 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.
>>
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>> You received this message because you are subscribed to the Google Groups
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>
> --
> 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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>
> --
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> version of the package, 2) to report the output of sessionInfo() and
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>
--
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.
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