[BioC] arrayQualityMetrics produces non-interactive PCA plot (Figure 3)
Wolfgang Huber
whuber at embl.de
Mon Dec 5 22:51:37 CET 2011
Dear Vladimir
thank you! I am glad it worked out.
The sensitive dependency on system dependencies (and our failure to
usefully diagnose when and when not they are fulfilled on a user's
system) is a big concern, although I see no easy short term solution to
change that.
Best wishes
Wolfgang
On 12/5/11 6:06 AM, Vladimir Zhurov wrote:
>> ...
>
> Dear Wolfgang,
>
> Thank you for such a quick reply.
>
> To answer your question, yes, there was a note generated after figure 3 legend:
> "Note: the figure is static - enhancement with interactive effects failed..."
>
> Ultimately, I have solved the problem. It was not locale (I have tried your
> suggestion to set everything to "C" and it did not change the result) but XML
> sub-system.
>
> The thing that fixed it was the installation of the latest version of libxslt
> from ftp://xmlsoft.org/libxml2/ (http://xmlsoft.org/).
>
> The complete procedure (but I do not know whether _every_ step except for
> libxslt was necessary in fact) involved:
>
> The latest stable cairo, cairomm (required additional installation of
> libsigc++-2.0-dev to build on Ubuntu 10.04.3) and pixman from
> http://cairographics.org/ (cairo needs pixman to compile, and I added
> cairomm to get to the same version level).
>
> And the latest libxml-2.0 and libxslt from http://xmlsoft.org/
>
> $ pkg-config --modversion cairo libxml-2.0 libxslt
> 1.10.2
> 2.7.8
> 1.1.26
>
> Recompiled all Bioconductor packages as per instructions on the main site.
>
> source("http://bioconductor.org/biocLite.R")
> pkgs<- rownames(installed.packages())
> biocLite(pkgs)
>
> ...and it worked.
>
> Below is the current working session info.
> And if you are still interested, I have broken report at:
>
> http://devbiol.zoo.uwo.ca/~vzhurov/MLL_A_Report_broken.tar.gz
>
>> sessionInfo()
>
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
> [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgu133acdf_2.9.1 AnnotationDbi_1.16.8
> [3] arrayQualityMetrics_3.10.0 ALLMLL_1.2.11
> [5] affy_1.32.0 Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.0
> [4] beadarray_2.4.1 BiocInstaller_1.2.1 Biostrings_2.22.0
> [7] Cairo_1.5-0 cluster_1.14.1 DBI_0.2-5
> [10] genefilter_1.36.0 grid_2.14.0 Hmisc_3.9-0
> [13] hwriter_1.3 IRanges_1.12.4 KernSmooth_2.23-7
> [16] lattice_0.20-0 latticeExtra_0.6-19 limma_3.10.0
> [19] preprocessCore_1.16.0 RColorBrewer_1.0-5 RSQLite_0.11.0
> [22] setRNG_2009.11-1 splines_2.14.0 survival_2.36-10
> [25] SVGAnnotation_0.9-0 tools_2.14.0 vsn_3.22.0
> [28] XML_3.6-1 xtable_1.6-0 zlibbioc_1.0.0
>
> Again, thank you for help and arrayQualityMetrics.
>
> Regards.
>
> Vladimir.
>
>> Wolfgang Huber<whuber at ...> writes:
>>
>> Dear Vladimir
>>
>> thank you for the precise report. This is peculiar, I just ran your
>> example script on a very similar installation (see below), and Figure 3,
>> the PCA plot, comes out as intended (i.e. interactive).
>>
>> Do you get the message "Note: the figure is static - enhancement with
>> interactive effects failed..." ?
>>
>> This is what I tried:
>>
>> $ uname -a
>> Darwin spinoza 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug 9 20:54:00
>> PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64
>>
>> $ pkg-config --modversion cairo libxml-2.0
>> 1.10.2
>> 2.7.8
>>
>> > sessionInfo()
>> R Under development (unstable) (2011-12-02 r57789)
>> Platform: x86_64-apple-darwin11.2.0/x86_64 (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] hgu133acdf_2.9.1 AnnotationDbi_1.17.9
>> [3] arrayQualityMetrics_3.11.0 ALLMLL_1.2.11
>> [5] affy_1.33.2 Biobase_2.15.2
>> [7] BiocGenerics_0.1.3 BiocInstaller_1.3.3
>> [9] fortunes_1.4-2
>>
>> loaded via a namespace (and not attached):
>> [1] Biostrings_2.23.4 Cairo_1.5-0 DBI_0.2-5
>> [4] Hmisc_3.9-0 IRanges_1.13.13 KernSmooth_2.23-7
>> [7] RColorBrewer_1.0-5 RSQLite_0.11.0 SVGAnnotation_0.9-0
>> [10] XML_3.6-1 affyPLM_1.31.0 affyio_1.23.1
>> [13] annotate_1.33.0 beadarray_2.5.2 cluster_1.14.1
>> [16] genefilter_1.37.0 grid_2.15.0 hwriter_1.3
>> [19] lattice_0.20-0 latticeExtra_0.6-19 limma_3.11.1
>> [22] preprocessCore_1.17.1 setRNG_2009.11-1 splines_2.15.0
>> [25] survival_2.36-10 tools_2.15.0 vsn_3.23.0
>> [28] xtable_1.6-0 zlibbioc_1.1.0
>>
>> There haven't been any relevant changes from arrayQualityMetrics_3.10.0
>> to arrayQualityMetrics_3.11.0, so only the potentially relevant
>> difference I can see is the locale. Can you try with "C"?
>>
>> Also, can you make the report that you get available, so I can see what
>> the differences in the generated SVG are to the one that I get. This
>> could then, potentially, be useful information for the maintainer of the
>> SVGAnnotation package (on which arrayQualityMetrics relies) if your
>> problem is indeed related to that.
>>
>> Thanks and best wishes
>> Wolfgang
>>
>> On 12/3/11 2:40 AM, Vladimir Zhurov wrote:
>>>> This is the first post, so I am not top-posting.
>>>
>>> Hello all,
>>>
>>> I am having a problem with the arrayQualityMetrics interactive
>>> SVG graphics.
>>> The system is Ubuntu 10.04.3 LTS. Viewing was done in Firefox 8 and
>>> Chrome 15.
>>>
>>> I would greatly appreciate any help with this issue.
>>>
>>> Below is the information about system, libraries version
>>> and sample R session.
>>>
>>> $ uname -a
>>> Linux 2.6.32-36-generic #79-Ubuntu SMP Tue Nov 8 22:29:53 UTC 2011
>>> x86_64 GNU/Linux
>>>
>>> $ pkg-config --modversion cairo libxml-2.0
>>> 1.10.2
>>> 2.7.8
>>>
>>> $ R --vanilla
>>>
>>> R version 2.14.0 (2011-10-31)
>>> Copyright (C) 2011 The R Foundation for Statistical Computing
>>> ISBN 3-900051-07-0
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>> Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> library("ALLMLL")
>>> Loading required package: affy
>>> Loading required package: Biobase
>>>
>>> Welcome to Bioconductor
>>>
>>> Vignettes contain introductory material. To view, type
>>> 'browseVignettes()'. To cite Bioconductor, see
>>> 'citation("Biobase")' and for packages 'citation("pkgname")'.
>>>
>>>> data("MLL.A")
>>>> library("arrayQualityMetrics")
>>>> arrayQualityMetrics(MLL.A,
>>> + outdir="MLL.A_Report",
>>> + force=TRUE,
>>> + do.logtransform=TRUE)
>>> The directory 'MLL.A_Report' has been created.
>>> Loading required package: AnnotationDbi
>>>
>>> KernSmooth 2.23 loaded
>>> Copyright M. P. Wand 1997-2009
>>>> traceback()
>>> No traceback available
>>>> warnings()
>>> NULL
>>>> sessionInfo()
>>> R version 2.14.0 (2011-10-31)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
>>> [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
>>> [7] LC_PAPER=C LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] hgu133acdf_2.9.1 AnnotationDbi_1.16.8
>>> [3] arrayQualityMetrics_3.10.0 ALLMLL_1.2.11
>>> [5] affy_1.32.0 Biobase_2.14.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.0
>>> [4] beadarray_2.4.1 BiocInstaller_1.2.1 Biostrings_2.22.0
>>> [7] Cairo_1.5-0 cluster_1.14.1 DBI_0.2-5
>>> [10] genefilter_1.36.0 grid_2.14.0 Hmisc_3.9-0
>>> [13] hwriter_1.3 IRanges_1.12.4 KernSmooth_2.23-7
>>> [16] lattice_0.20-0 latticeExtra_0.6-19 limma_3.10.0
>>> [19] preprocessCore_1.16.0 RColorBrewer_1.0-5 RSQLite_0.11.0
>>> [22] setRNG_2009.11-1 splines_2.14.0 survival_2.36-10
>>> [25] SVGAnnotation_0.9-0 tools_2.14.0 vsn_3.22.0
>>> [28] XML_3.6-1 xtable_1.6-0 zlibbioc_1.0.0
>>>
>>> More details that I had to move down here due to "top-posting" error from
>>> the
>>> web form interface.
>>> I apologize for the inconvenience.
>>> How is one supposed to post a R session?
>>>
>>> Only figure 3 is broken, figures 6 and 12 are interactive.
>>> I have attempted
>>> previously discussed fixes such as updating cairo and libxml.
>>>
>>> _______________________________________________
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>>> Bioconductor at ...
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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