[BioC] arrayQualityMetrics not producing all diagnostic plots

[Martin Morgan]

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

> 
> 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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