Entering edit mode
James F. Reid
▴
610
@james-f-reid-3148
Last seen 10.3 years ago
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).
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
>