[BioC] arrayQualityMEtrics

[Guillaume Meurice]

Dear All,

I encounter the following probleme with arrayQualityMetrics (v3.8.0) : 

> arrayQualityMetrics(RG, outdir="aqmRaw", do.logtransform=T)
The report will be written into directory 'aqmRaw'. 
Error in eval(expr, envir, enclos) : could not find function "note"
Error in prepdata(expressionset, intgroup = intgroup, do.logtransform = do.logtransform) : 
  Argument 'expressionset' is of class 'RGList', and its automatic conversion into 'NChannelSet' failed. Please try to convert it manually.

my object RG is an RGList : 

> class(RG)
[1] "RGList"
attr(,"package")
[1] "limma"
> 

here the sessionInfo : 


> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] mclust_3.4.8              MASS_7.3-12               RColorBrewer_1.0-2        lattice_0.19-23           foreign_0.8-43            multicore_0.1-5          
 [7] pvclust_1.2-2             arrayQualityMetrics_3.8.0 impute_1.26.0             marray_1.30.0             limma_3.8.1              

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.14.1  Biobase_2.12.1        Biostrings_2.20.0     Cairo_1.4-9           DBI_0.2-5             Hmisc_3.8-3           IRanges_1.10.0       
 [8] KernSmooth_2.23-4     RSQLite_0.9-4         SVGAnnotation_0.9-0   XML_3.4-0             affy_1.30.0           affyPLM_1.28.5        affyio_1.20.0        
[15] annotate_1.30.0       beadarray_2.2.0       cluster_1.13.3        genefilter_1.34.0     grid_2.13.0           hwriter_1.3           latticeExtra_0.6-14  
[22] preprocessCore_1.14.0 setRNG_2009.11-1      splines_2.13.0        survival_2.36-9       tools_2.13.0          vsn_3.20.0            xtable_1.5-6      


thanks for any help
--
Guillaume