[BioC] unable to find an inherited method for function "arrayQualityMetrics", for signature "vsn"

[Wolfgang Huber]

Ciao Giovanni,

The arrayQualityMetrics function expects an ExpressionSet (or similar). 
The output of vsn2 is an object of class 'vsn' that contains the model 
fitting parameters. Please use the function 'justvsn' to make it produce 
the transformed ExpressionSet.

This is also explained in the vignette 'Introduction to vsn' in the very 
first few paragraphs.

	Best wishes
	Wolfgang


Tonon Giovanni ha scritto:
> I am trying to perform some QC on affymetrix array data using the arrayQualityMetrics.
> 
> I get the following error:
> qm_vsn <- arrayQualityMetrics(expressionset = thal_vsn, outdir = "/home/testout/vsn2", do.logtransform = FALSE)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "arrayQualityMetrics", for signature "vsn"
> 
> Could somebody kindly help?
> Thanks!
> Giovanni
> 
> Here is the complete code
> library("affy")
> thal <- ReadAffy()
> library("arrayQualityMetrics")
> library("vsn")
> thal_vsn <- vsn2(thal)
> qm_vsn <- arrayQualityMetrics(expressionset = thal_vsn, outdir = "/home/testout/", do.logtransform = FALSE)
> 
> -----------------------------------------------------------------
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-- 

Best wishes
      Wolfgang

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