[BioC] arrayQualityMetrics not producing all diagnostic plots
Benilton Carvalho
beniltoncarvalho at gmail.com
Thu Oct 28 15:27:55 CEST 2010
btw, don't worry about my affyio version... i know i'm doing something
i shouldn't. b
On 28 October 2010 14:23, Benilton Carvalho <beniltoncarvalho at gmail.com> wrote:
> For the record, I can't reproduce the issue, but my libxml2 is 2.7.3
>
> sessionInfo() is shown below:
>
> R version 2.12.0 Patched (2010-10-21 r53386)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] hgu133acdf_2.7.0 arrayQualityMetrics_3.2.0
> [3] vsn_3.18.0 affyPLM_1.26.0
> [5] preprocessCore_1.12.0 gcrma_2.22.0
> [7] ALLMLL_1.2.8 affy_1.28.0
> [9] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.19.1 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_1.8.0 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 tools_2.12.0 XML_3.2-0
> [25] xtable_1.5-6
>
>
> On 28 October 2010 14:16, James F. Reid <james.reid at ifom-ieo-campus.it> wrote:
>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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>>>>
>>
>
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