[BioC] arrayQualityMetrics not producing all diagnostic plots
Martin Morgan
mtmorgan at fhcrc.org
Wed Oct 27 16:41:16 CEST 2010
On 10/27/2010 06:16 AM, James F. Reid wrote:
> 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!
Hi James --
Hmm. For what it's worth, I don't have problems with a similar set of
packages. I have
> capabilities()
jpeg png tiff tcltk X11 aqua http/ftp sockets
TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
libxml fifo cledit iconv NLS profmem cairo
TRUE TRUE TRUE TRUE TRUE FALSE TRUE
What does traceback() say after the error? Do you have the cdf for this
package (hgu133acdf_2.7.0; library('hgu133acdf') already installed? The
installation warning for XML is not likely the problem.
Martin
>
> 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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>>
>>
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