[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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