[BioC] arrayQualityMetrics not producing all diagnostic plots
James F. Reid
james.reid at ifom-ieo-campus.it
Thu Oct 28 14:36:57 CEST 2010
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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