[BioC] Affy EXON Array: iterPLIER or RMA

[Daniel Brewer]

Hi,

I am doing some analysis on the Affymetrix Exon human microarrays.
Normally I would use RMA to summarize, but in the papers by Affymetrix
they use iterPLIER for the gene-level estimates and PLIER for the
Exon-level estimates.

Is it ok to use RMA for both summary levels for these arrays?
Does anyone have an opinion on what the best approach to use is?

Also does anyone use DABG to filter out badly detected probes?

Thanks

Daniel

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