[BioC] missing figure text in arrayQualityMetrics

[Wolfgang Huber]

Dear Daniel

thanks. I have not seen this type of problem before and am not sure 
exactly what your problem is. Can you send me (perhaps offline) the 
script that you use to produce the report, the report itself (tar-zipped 
directory), and ideally the data set (you can anonymize the samples / 
genes).

Also, the output of
    pkg-config --modversion cairo

	Best wishes
	Wolfgang

Jul/4/12 1:56 PM, Daniel Aaen Hansen scripsit::
> Hi,
>
> I just noticed that the axis labels, title and legend text have gone missing on some of the plots in the quality report. In fact I am not sure which upgrade caused the problem. More specifically, it is the three interactive plots that are missing text labels. The interactive mouse-over text works fine, it is only the static text that is missing from:
>
> Figure 3: Principal Component Analysis.
> Figure 6: Density plots.
> Figure 12: RNA digestion plot.
>
> Is anyone else having this problem? Or am I missing some dependencies in my installation (see below)? I am using the most recent development version of arrayQualityMetrics.
>
> Best,
> Daniel
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 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  methods   base
>
> other attached packages:
> [1] arrayQualityMetrics_3.13.5
>
> loaded via a namespace (and not attached):
>   [1] affy_1.34.0           affyio_1.24.0         affyPLM_1.32.0
>   [4] annotate_1.34.0       AnnotationDbi_1.18.1  beadarray_2.6.0
>   [7] BeadDataPackR_1.8.0   Biobase_2.16.0        BiocGenerics_0.2.0
> [10] BiocInstaller_1.4.7   Biostrings_2.24.1     Cairo_1.5-1
> [13] cluster_1.14.2        colorspace_1.1-1      DBI_0.2-5
> [16] genefilter_1.38.0     grid_2.15.1           Hmisc_3.9-3
> [19] hwriter_1.3           IRanges_1.14.3        lattice_0.20-6
> [22] latticeExtra_0.6-19   limma_3.12.1          plyr_1.7.1
> [25] preprocessCore_1.18.0 RColorBrewer_1.0-5    reshape2_1.2.1
> [28] RSQLite_0.11.1        setRNG_2011.11-2      splines_2.15.1
> [31] stats4_2.15.1         stringr_0.6           survival_2.36-14
> [34] SVGAnnotation_0.9-0   vsn_3.24.0            XML_3.9-4
> [37] xtable_1.7-0          zlibbioc_1.2.0
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber