[BioC] arrayQualityMetrics error with MAList

[Wolfgang Huber]

Dear Karen

in fact, there is no coercion method from MAList to NChannelSet, yet 
there is one from MAList to ExpressionSet (and all that actually makes 
sense). Thus, can you please try

library(convert)
MA.avg_TEST1_eSet <- as(MA.avg_TEST1, 'ExpressionSet')
arrayQualityMetrics(MA.avg_TEST1_eSet, outdir="Test1_report")

Let me know if that works. Sometimes it happens that this fails with an 
error, since the metadata in limma MALists tends to be less strictly 
organised than what is expected by Biobase. In that case, send me the 
offending object, and I will try to tweak the coercion method to deal 
with it.

	Best wishes
	Wolfgang
	



Mar/1/12 9:48 PM, Wolfgang Huber scripsit::
> 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.
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
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>
>


-- 
Best wishes
	Wolfgang

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