[BioC] Problems using arrayQualityMetrics

[Wolfgang Huber]

Dear Syed

thanks! With what version of 'arrayQualityMetrics' did you experience 
this? As far as I can tell, the function 'annotateSvgMatplot' was last 
used in Bioconductor release 2.7 from autumn 2010.

To use this package, please, please use a *current version of R, 
Bioconductor, and the cairo graphics* library.

Please do not expect that any old combination of these components will 
work together. Also, you would be missing out on the cool new features.

I recommend using 
http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html, 
which is close to release.

PS - OKish looking plots are one thing, but SVGAnnotation postprocesses 
the SVG code for the plots and requires that that code is quite 
precisely as expected.

Enjoy,
	Wolfgang

Mar/23/12 1:04 AM, Syed Haider scripsit::
> Dear Wolfgang,
>
> Ros's computer definitely needs an upgrade. However, looking breifly
> into this, here is the offending line of code from
> arrayQualityMetrics::aqm.report.qm(...)
>
> size = annotateSvgMatplot(svgtemp, nameimg, annotationInfo=qm$svg)
>
> The above fails while generating pca.svg and rnadeg.svg. Interestingly
> density.svg comes out *okish*. The density plot looks correct but
> without axis-labels and legends. All other figures are fine too,
> including the pdf equivalent of all svgs.
>
>
> Best,
> Syed
>
>
> On 22/03/2012 23:39, Wolfgang Huber wrote:
>> Dear Rosalind
>>
>> unfortunately, the fact that the package manager on your Redhat Linux
>> does not provide you with a newer version does not mean that there is
>> none. The Linux distribution that you are using seems to be very much
>> behind in time: cairo 1.2.4 is from 2006, see http://cairographics.org/
>>
>> Two options:
>> - use a system that is better kept up-to-date
>> - remove the cairo that your package manager gives you, and install
>> libcairo >=1.10.2 'manually' by downloading it from the above URL.
>>
>> Btw, I would also also prefer if arrayQualityMetrics (i.e., really the
>> SVGAnnotation package) was backwards compatible with any old version of
>> cairo, but that is not a realistic expectation (neither for our
>> software, nor for many other products, incl. commercial).
>>
>> Best wishes
>> Wolfgang
>>
>> Mar/22/12 12:38 PM, Rosalind Cutts scripsit::
>>> Thanks very much for the reply, I have tried this with a clean R and
>>> bioconductor installation and get a similar error.
>>>
>>> ArrayQualityMetrics works ok, it just fails to produce some of the
>>> graphical output.
>>>
>>> Cairo version:
>>> pkg-config --modversion cairo
>>> 1.2.4
>>>
>>> When I tried updating Cairo on the Redhat linux machine I am using as
>>> suggested by your link there were no updates to load.
>>>
>>> Is there anything else that you could suggest I could try.
>>>
>>> Thanks again for your help
>>>
>>> Ros
>>
>>
>> Wolfgang Huber
>> EMBL
>> http://www.embl.de/research/units/genome_biology/huber
>>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber