[BioC] arrayQualityMetrics error

[Wolfgang Huber]

Dear Paulo

there have been many improvements on the package since the last release, 
and I would recommend trying the devel version >=3.4.8

http://bioconductor.org/help/bioc-views/2.8/bioc/html/arrayQualityMetrics.html

which afaIcs will run well on R 2.12. One of the advantages is that it 
uses Simon Urbanek's "Cairo" package, which brings its own cairo library 
rather than relying on what it finds on the host system [1] - this 
should solve your problem.

The package is in a state of beta-testing, with
- the presentation of the outlier detection in the reports not yet fully 
cooked,
- and I am not yet sure whether & how well it works on 64bit Windows.

I hope to finalise this within a week or three; any user experiences and 
comments are welcome.

A sneal preview of the new reports is here [2].

	Wolfgang


[1] 
https://stat.ethz.ch/pipermail/bioconductor/attachments/20110128/ca068c82/attachment.pl
[2] 
http://www-huber.embl.de/users/whuber/pub/Report%20for%20nCCl4%20with%20RIN


Paulo Nuin scripsit 10/02/11 02:10:
> Hi James
>
> I checked our Cairo version, and it seems quite old. I'm checking the best way to update, as we are using CentOS official package. If the problem persists after upgrade, I will report to the list.
>
> Thanks a lot for your help.
>
> Paulo
>
>
> On 2011-02-09, at 4:03 PM, James F. Reid wrote:
>
>> Hi Paulo,
>>
>>
>> On 02/09/2011 09:38 PM, Paulo Nuin wrote:
>>> Hi everyone
>>>
>>> We just got a new HPC system to speed up our analysis, but we are having some problems with the end part of a arrayQualityMetrics run.
>>>
>>> It goes fine until section 5, were it is interrupted by an error
>>>
>>>> arrayQualityMetrics(rawAffyData, outdir="quality", force=T)
>>> The report will be written into directory 'quality'.
>>> [[1]]
>>>
>>> [[2]]
>>>
>>> [[3]]
>>>
>>> [[4]]
>>>
>>> Error in UseMethod("xmlAttrs", node) :
>>>    no applicable method for 'xmlAttrs' applied to an object of class "NULL"
>>> In addition: There were 39 warnings (use warnings() to see them)
>>
>> The same happened on my system, the problem was a very old version of cairo, see this thread:
>> https://stat.ethz.ch/pipermail/bioconductor/2010-October/036143.html
>> Either upgrade if you can or try using the devel version which I believe detects the capabilites of the system before running and producing annotated svg figures or not.
>>
>> HTH,
>> James.
>>
>>
>>
>>>
>>> Our sessionInfo and capabilities are below. R is compiled natively and most of the required libraries are present and compiled with the system. Any help is appreciated.
>>>
>>> Cheers
>>> Paulo
>>>
>>>> capabilities()
>>>      jpeg      png     tiff    tcltk      X11     aqua http/ftp  sockets
>>>      TRUE     TRUE     TRUE    FALSE     TRUE    FALSE     TRUE     TRUE
>>>    libxml     fifo   cledit    iconv      NLS  profmem    cairo
>>>      TRUE     TRUE     TRUE     TRUE     TRUE    FALSE     TRUE
>>>
>>>
>>>
>>>> sessionInfo()
>>> R version 2.12.1 (2010-12-16)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] hgu133plus2cdf_2.7.0      arrayQualityMetrics_3.2.4
>>> [3] vsn_3.18.0                affyPLM_1.26.0
>>> [5] preprocessCore_1.12.0     gcrma_2.22.0
>>> [7] affy_1.28.0               Biobase_2.10.0
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] affyio_1.18.0        annotate_1.28.0      AnnotationDbi_1.12.0
>>>   [4] beadarray_2.0.3      Biostrings_2.18.2    DBI_0.2-5
>>>   [7] genefilter_1.32.0    grid_2.12.1          hwriter_1.3
>>> [10] IRanges_1.8.8        KernSmooth_2.23-4    lattice_0.19-13
>>> [13] latticeExtra_0.6-14  limma_3.6.9          marray_1.28.0
>>> [16] RColorBrewer_1.0-2   RSQLite_0.9-4        simpleaffy_2.26.1
>>> [19] splines_2.12.1       stats4_2.12.1        survival_2.36-2
>>> [22] SVGAnnotation_0.7-2  tools_2.12.1         XML_3.2-0
>>> [25] xtable_1.5-6
>>>
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>
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-- 


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