[BioC] Best way to do quality control and analysis on Exon arrays

[Daniel Brewer]

Hi,

I have played around with small Exon 1.0 ST datasets before and have
been generally been using affymetrix power tools (APT) to do the
summarisation and then the Affymetrix annotation using the "core" set.
I am about to start on a larger set of analysis and so I am revisiting
what are the best tools to use.  There now seems to be three main
alternatives with R to do the summarisation and one outside R.  A couple
of questions:

1)  What is the best way to do quality control on these arrays?  I was
thinking about looking at the spread of DABG p-values but for exonmap at
least it doesn't seem like you can calculate these values.  Can you use
AffyQCreport?

2) If I decided to use APT for the summarisation are there annotation
packages available?  exonmap seems to be have an annotation but this
seems to be redone, is there any based on the affy supplied annotations
and the "core" and "extended" groups?

Thanks

Dan

-- 
**************************************************************
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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