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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