[BioC] Problems using arrayQualityMetrics

[Syed Haider]

Thanks Wolfgang for your detailed reply.

The machine which i tried this on had:

arrayQualityMetrics v3.2.4 (installed from source)
R v2.12.2
System wide Cairo v1.2.4
R Cairo v1.5-1

I guess Ros et al have tried this on the latest versions too.

Thanks,
Syed



On 23/03/2012 08:12, Wolfgang Huber wrote:
> 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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>
>