[BioC] Is a change in kit significant?

[Daniel Brewer]

Hi

I have a set of Affymetrix Exon data which has about 40 samples.  The
last third of the samples have used a different kit for the experiment,
and I have been asked to determine whether the change in kit is significant.

I have done clustering and PCA and the results suggest it does make a
different, but I would like to put some sort of statistic on it.  What
is the best way to do this?  I would think maybe this is a limma type
problem but I am not sure how to get an overall statistic rather than
just for individual probes.

Many thanks

Dan

-- 
**************************************************************
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
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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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