[BioC] arrayQualityMetrics not producing all diagnostic plots
Benilton Carvalho
beniltoncarvalho at gmail.com
Thu Oct 28 15:06:29 CEST 2010
what do you get for
xml2-config --version
?
On 28 October 2010 13:36, James F. Reid <james.reid at ifom-ieo-campus.it> wrote:
> Hi Martin,
>
> On 10/27/2010 04:41 PM, Martin Morgan wrote:
>>
>> 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.
>
> I have the same capabilities() on my platform.
> Here is the output of traceback() together with my sessionInfo.
>
> Error in UseMethod("xmlAttrs", node) :
> no applicable method for 'xmlAttrs' applied to an object of class "NULL"
>
>> traceback()
> 18: xmlAttrs(node, addNamespace)
> 17: xmlGetAttr(clipPath[["path"]], "d")
> 16: getRect(xmlGetAttr(clipPath[["path"]], "d"))
> 15: getPlotRegion(n)
> 14: FUN(X[[1L]], ...)
> 13: lapply(X, FUN, ...)
> 12: sapply(tmp, function(n) all(getPlotRegion(n) == vb))
> 11: getPlotRegionNodes(doc)
> 10: is.vector(X)
> 9: lapply(getPlotRegionNodes(doc), getPlotPoints)
> 8: getPlotPoints.XMLInternalDocument(doc)
> 7: annotationInfo$getfun(doc)
> 6: aqm.highlight(doc, annotationInfo = annotationInfo)
> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg)
> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
> 3: aqm.writereport(reporttitle, expressionset, obj)
> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
> do.logtransform = TRUE)
> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
> do.logtransform = TRUE)
>
>> 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] hgu133acdf_2.7.0 ALLMLL_1.2.8
> [3] arrayQualityMetrics_3.2.0 vsn_3.18.0
> [5] affyPLM_1.26.0 preprocessCore_1.12.0
> [7] gcrma_2.22.0 affy_1.28.0
> [9] 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_1.8.2 KernSmooth_2.23-4 lattice_0.19-13
> [13] latticeExtra_0.6-14 limma_3.6.5 marray_1.28.0
> [16] RColorBrewer_1.0-2 RSQLite_0.9-2 simpleaffy_2.26.0
> [19] splines_2.12.0 stats4_2.12.0 survival_2.35-8
> [22] SVGAnnotation_0.6-0 XML_3.2-0 xtable_1.5-6
>
> On another machine with the same sessionInfo I get another error:
> Error in aqm.highlight(doc, annotationInfo = annotationInfo) :
> 'length(annotationInfo$annotation)' must be equal to 'length(series)', the
> #number of objects in the plot.
>
>> traceback()
> 7: stop("'length(annotationInfo$annotation)' must be equal to
> 'length(series)', the number of objects in the plot.")
> 6: aqm.highlight(doc, annotationInfo = annotationInfo)
> 5: annotateSvgMatplot(svgtemp, nameimg, annotationInfo = qm$svg)
> 4: aqm.report.qm(p, obj[[i]], i, names(obj)[i])
> 3: aqm.writereport(reporttitle, expressionset, obj)
> 2: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
> do.logtransform = TRUE)
> 1: arrayQualityMetrics(expressionset = MLL.A, outdir = "MLL", force = TRUE,
> do.logtransform = TRUE)
>
> Can someone help?
>
> Thanks.
> James.
>
>>
>> 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
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>
>>
>
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