[BioC] Normalising to Agilent controls in a two-colour experiment

[Daniel Brewer]

Hello,

I am currently working on a rather strange project where amoeba along
with a human cell line have been hybridised to an Agilent 4x44k
microarray.  As I wouldn't expect the majority of probes for the amoeba
sample to be expressed, the assumption for LOESS that on average there
isn't any difference between samples does not hold.  So as an
alternative I have considered normalising LOESS but only using the
Agilent control probes.  Is this reasonable? or is there a better approach?

Also does anyone know what all the types of control probes on the
Agilent array are?

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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