[BioC] arrayQualityMetrics not producing all diagnostic plots

[James F. Reid]

Dear Martin,

On 27/10/2010 14:17, Martin Morgan wrote:
> On 10/27/2010 02:26 AM, James F. Reid wrote:
>> Dear all,
>>
>> Since upgrading to the latest version of Bioconductor, I am having
>> problems using the package arrayQualityMetrics because it does not
>> produce a full report (both for single and double channels arrays).
>
> HI James -- have you tried updating your installed packages? I notice
> below that you are using the 'release' version of R (2.12.0) but that
> many of your packages are from a previous 'devel' version of
> Bioconductor (odd-numbered second version field, e.g., Biobase 2.9.2).
>
> See
>
> http://bioconductor.org/install/index.html#update-bioconductor-packages
>
> Martin
>

you're right and I should have updated my packages before sending a mail 
to the list. However even after updating the problem remains. The error 
message points to a problem using the library XML. When installing XML I 
noticed the following:
Creating a new generic function for "source" in "XML"
Warning in .NonstandardGenericTest(body(fdef), name, stdGenericBody) :
   the supplied generic function definition for xmlClone does not seem 
to call 'standardGeneric'; no methods will be dispatched!

Any ideas?
James.

My updated session:
 > sessionInfo()
R version 2.12.0 (2010-10-15)
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  tools     methods
[8] base

other attached packages:
[1] arrayQualityMetrics_3.2.0 vsn_3.18.0
[3] affyPLM_1.26.0            preprocessCore_1.12.0
[5] gcrma_2.22.0              affy_1.28.0
[7] 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_2.0.1      Biostrings_2.18.0    DBI_0.2-5
  [7] genefilter_1.32.0    grid_2.12.0          hwriter_1.2
[10] IRanges_1.8.1        lattice_0.19-13      latticeExtra_0.6-14
[13] limma_3.6.4          marray_1.28.0        RColorBrewer_1.0-2
[16] RSQLite_0.9-2        simpleaffy_2.26.0    splines_2.12.0
[19] stats4_2.12.0        survival_2.35-8      SVGAnnotation_0.6-0
[22] XML_3.2-0            xtable_1.5-6


>>
>> Thanks.
>> James.
>>
>> Here is the first example from the arrayQualityMetrics vignette
>> (inst/scripts/arrayQualityMetrics.Rnw)
>>
>> library("ALLMLL")
>> data("MLL.A")
>>
>> library("arrayQualityMetrics")
>> arrayQualityMetrics(expressionset = MLL.A,
>>                      outdir = "MLL",
>>                      force = TRUE,
>>                      do.logtransform = TRUE)
>>
>> produces:
>> Error in UseMethod("xmlAttrs", node) : no applicable method for
>> 'xmlAttrs' applied to an object of class "NULL"
>>
>> without producing all the plots (stops after section 3: Between array
>> comparison), the html report is truncated.
>>
>>> sessionInfo()
>> R version 2.12.0 (2010-10-15)
>> 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  tools     methods
>> [8] base
>>
>> other attached packages:
>> [1] ALLMLL_1.2.8              arrayQualityMetrics_3.2.0
>> [3] vsn_3.17.2                affyPLM_1.25.1
>> [5] preprocessCore_1.11.0     gcrma_2.21.1
>> [7] affy_1.27.3               Biobase_2.9.2
>>
>> loaded via a namespace (and not attached):
>>   [1] affyio_1.17.4         annotate_1.27.3       AnnotationDbi_1.11.10
>>   [4] beadarray_2.0.1       Biostrings_2.17.48    DBI_0.2-5
>>   [7] genefilter_1.31.2     grid_2.12.0           hwriter_1.2
>> [10] IRanges_1.7.40        lattice_0.19-13       latticeExtra_0.6-14
>> [13] limma_3.5.21          marray_1.27.0         RColorBrewer_1.0-2
>> [16] RSQLite_0.9-2         simpleaffy_2.25.0     splines_2.12.0
>> [19] stats4_2.12.0         survival_2.35-8       SVGAnnotation_0.6-0
>> [22] XML_3.2-0             xtable_1.5-6
>>>
>>
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>
>