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karen power
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10
@karen-power-5140
Last seen 10.0 years ago
Hi,
I'm trying to use arrayQualityMetrics to investigate 2 colour Agilent
microarrays. However I get the following error;
> arrayQualityMetrics(MA.avg_TEST1, outdir="Test1_report")
The report will be written into directory 'Test1_report'.
Error in as(expressionset, "NChannelSet") :
no method or default for coercing "MAList" to "NChannelSet"
Error in prepdata(expressionset, intgroup = intgroup, do.logtransform
=
do.logtransform) :
Argument 'expressionset' is of class 'MAList', and its automatic
conversion
into 'NChannelSet' failed. Please try to convert it manually.
I have no idea how to succesfully turn an MAList into NChannelSet as
"MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet')"
doesn't work.
Is it something I'm doing wrong with the arrayQualityMetrics command?
Or else is
there a way around it? Session is as follows;
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] arrayQualityMetrics_3.10.0 BiocInstaller_1.2.1 limma_3.10.2
loaded via a namespace (and not attached):
[1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0
annotate_1.32.1 AnnotationDbi_1.16.18 beadarray_2.4.1
Biobase_2.14.0
Biostrings_2.22.0
[9] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5
genefilter_1.36.0 grid_2.14.2 Hmisc_3.9-2
hwriter_1.3
IRanges_1.12.6
[17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0
RColorBrewer_1.0-5 RSQLite_0.11.1 setRNG_2009.11-1
splines_2.14.2
survival_2.36-12
[25] SVGAnnotation_0.9-0 tools_2.14.2 vsn_3.22.0
XML_3.9-4
xtable_1.7-0 zlibbioc_1.0.0
Regards,
Karen
Karen Power BSc PhD
Room 039,
UCD Centre for Food Safety,
School of Public Health, Physiotherapy and Population Science
Veterinary Sciences Centre,
University College Dublin,
Belfield,
Dublin 4,
Ireland.
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