[BioC] arrayQualityMetrics not producing all diagnostic plots

Benilton Carvalho beniltoncarvalho at gmail.com
Thu Oct 28 15:23:55 CEST 2010


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
>>> 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
>>>
>



More information about the Bioconductor mailing list