[BioC] Quality control on Human Affymetrix Exon microarrays

Daniel Brewer daniel.brewer at icr.ac.uk
Wed Aug 4 16:58:39 CEST 2010

Hello Wolfgang,

Well I want to do two things primarily.  Firstly, look at the variation
of the probes in the probeset (Fit affyplm and look at the Normalized
Unscaled Standard Errors (NUSE)) and see if any of the arrays have
unusually high values.  Secondly, some how look at the images to see if
there are any unusual artifacts (I am attempting to do this with xps
with some success).



On 03/08/2010 9:41 PM, Wolfgang Huber wrote:
> 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


Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
15 Cotswold Road
Sutton, Surrey SM2 5NG
United Kingdom

Tel: +44 (0) 20 8722 4109


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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