[BioC] Quality control on Human Affymetrix Exon microarrays

[Wolfgang Huber]

Hi Daniel

before asking "how" it is often useful to ask "why".
I.e., what aspect of "quality" do you want to assess or measure using 
the probe level data?

  Best wishes
	Wolfgang

On Aug/2/10 12:13 PM, Daniel Brewer wrote:
> Hello,
>
> I normally use affymetrix power tools to summarise Human Affymetrix Exon
> microarrays and do QC type stuff on the summarised data, but I have now
> gained access to a machine with a lot more memory and so would like to
> do some quality control on the probe level data.
>
> For U133 type arrays I would create an affybatch object and then apply
> affyPLM and affyQCreport.  I read somewhere that affyWCreport does tests
> that aren't relevant to exon arrays, but how does one go about using
> affyPLM?
>
> What are other people doing for QC on exon arrays.
>
> Many thanks
>
> Dan
>

-- 


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