[BioC] arrayQualityMetrics produces non-interactive PCA plot (Figure 3)
Vladimir Zhurov
vzhurov2 at uwo.ca
Mon Dec 5 06:06:04 CET 2011
> ...
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 ...
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> > Search the archives:
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