[BioC] arrayQualityMEtrics

[Guillaume Meurice]

Dear Wolfgang,

many thanks for your answer, and you were right : loading Biobase solved the problem.

Best regards
--
Guillaume

> 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
> 
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