[BioC] arrayQualityMetrics not producing all diagnostic plots
James F. Reid
james.reid at ifom-ieo-campus.it
Thu Oct 28 15:16:02 CEST 2010
Hi,
On 10/28/2010 03:06 PM, Benilton Carvalho wrote:
> what do you get for
>
> xml2-config --version
>
> ?
on the machine that produces the xml based error
xml2-config --version
2.6.26
whereas on the machine that complains about
length(annotationInfo$annotation) I have a newer version:
2.7.7
James.
>
> 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
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
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>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>>>>
>>>>>
>>>
>>>
>>
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