[BioC] Normalisation of Agilent microRNA arrays using inbuilt controls?

[Daniel Brewer]

Hello,

I have been trying to work out the best way to normalise microRNA
microarrays recently as there seems to be some debate about whether the
normal mRNA assumptions hold.

The AgiMicroRna suggests using quantile or scale, whereas other posts I
have read have suggested VSN.

My question is whether the control probes on the Agilent chip could be
used o do the normalisation i.e. the Negative and Positive Control probes.

Would this be a good idea?  And how would one go about this? A loess
using the weights to define what probes are used?

Thanks

Dan

-- 
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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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