[BioC] Problem with NChannelSet objects using Agilent Data with arrayQualityMetrics package
Laurent.Pays
Laurent.Pays at univ-lyon1.fr
Wed Feb 26 17:43:36 CET 2014
Hi to all,
After downloading Agilent Data using the ArrayExpress package:
>> AEset <-ArrayExpress("E-GEOD-32915”)
I verified that AEset was indeed a NChannelSet object:
> > class(AEset)
> [1] "NChannelSet"
> attr(,"package")
> [1] “Biobase"
Then I tried to use the arrayQualityMetrics package which should work on NChannelSet objects:
> arrayQualityMetrics ( AEset )
But I get this error message:
> The report will be written into directory 'arrayQualityMetrics report for AEset'.
> Erreur dans platformspecific(expressionset, intgroup, do.logtransform) :
> 'assayData(expressionset)' must contain either 'exprs', or 'R' and 'G', but not both.
My question is how do I get pass this error, or at least or can I remove either ‘exprs’, or ‘R’ and ‘G’ from the NChannelSet object knowing that when I try:
> > channelNames(AEset)
I only get:
> [1] "E" “Eb”
and I don’t know what to analyse with arrayQualityMetrics: “E” or “Eb”?
Thanks in advance to your answers
Laurent
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