[BioC] Quality control on Human Affymetrix Exon microarrays

Daniel Brewer daniel.brewer at icr.ac.uk
Mon Aug 2 12:13:20 CEST 2010


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

What are other people doing for QC on exon arrays.

Many thanks


Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

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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