[BioC] arrayQualityMEtrics

[Wolfgang Huber]

Dear Guillaume

Can you try again after:
   library("Biobase")

What seems to happen is the following: arrayQualityMetrics wants to 
convert your object 'RG' into an 'NChannelSet'. The conversion function 
for doing so resides in the package vsn, and usually works. However, for 
your particular object, an information message is triggered, which is 
supposed to be written with the 'note' function from Biobase. It appears 
that I have failed to import that into vsn. This will be fixed in 
Bioc-devel in vsn >= 3.21.1.

(Perhaps I relied too much on codetools / 'R CMD check' noticing such 
things - which they apparently fail to do in this case.)

Best wishes
	Wolfgang

Guillaume Meurice scripsit 05/25/2011 04:27 PM:
> 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
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-- 


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