[BioC] arrayQualityMetrics produces non-interactive PCA plot (Figure 3)
Wolfgang Huber
whuber at embl.de
Sun Dec 4 02:33:15 CET 2011
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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--
Best wishes
Wolfgang
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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