[BioC] arrayQualityMetrics not producing all diagnostic plots

Fri Oct 29 00:18:09 CEST 2010

Hi James,

1.) the "length(annotationInfo$annotation)" complaint is (as far as I 
currently understand it) related to a version incompatibility between 
newer versions of libcairo on your computer and the SVGAnnotation 
package. I am working with Duncan to sort this out. (See also 
https://stat.ethz.ch/pipermail/bioconductor/2010-October/035958.html)

What is the output of:
    pkg-config --modversion cairo
on both of your machines?

2.) I have never seen the other error you report (about something being 
NULL that should be an XML-node), but it smells like it could be a 
consequence of the same underlying problem: format or content of an SVGH 
graphics file (which is an XML document) that is not expected by 
SVGAnnotation.

I am sorry that this functionality is so brittle. When it works, it is 
great, see e.g. 
http://www-huber.embl.de/users/whuber/arrayQualityMetrics-Reports/CCl4-RIN/QMreport.html 
Figures 4, 6 and 
http://www-huber.embl.de/users/whuber/arrayQualityMetrics-Reports/MLL/QMreport.html 
Figs. 4, 6, 8. I am working right now on making it more robust!

For now, all I can offer is the workaround already suggested in the 21 
Oct post. Sorry for that, this seems to be the cost of being 'cutting-edge'.

	Best wishes
	Wolfgang

Il Oct/28/10 3:16 PM, James F. Reid ha scritto:
> 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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>>>>>>
>>>>>>
>>>>
>>>>
>>>
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