[BioC] arrayQualityMetrics error with MAList

[Wolfgang Huber]

Dear Karen

what happens when you run

   library("convert")

before

   MA.avg_TEST1_nChannel<-as(MA.avg_TEST1, 'NChannelSet')

If that does not help, can you please send me (offline) the offending 
object 'MA.avg_TEST1'?

I suspect I need to fix the NAMESPACE of arrayQualiyMetrics, sorry for that.

	best wishes
	Wolfgang

Mar/1/12 3:45 PM, karen power scripsit::
> 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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>
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-- 
Best wishes
	Wolfgang

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