[BioC] Normalize data across platforms

Priscila Darakjian darakjia at ohsu.edu
Tue Mar 31 18:35:16 CEST 2009

Maybe this will help you regarding control probes across platforms --> https://aberdeen.ac.uk/ims/facilities/microarray/documents/chipcontrols.doc


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Steve Taylor
Sent: Tuesday, March 31, 2009 7:46 AM
To: michael watson (IAH-C)
Cc: Bioconductor
Subject: Re: [BioC] Normalize data across platforms


Thanks for your reply.

> Quantile normalisation is a very conservative normalisation, and there are fears in some quarters that it may lead to over-normalisation.  However, as you're comparing between datasets, this may be what you're after.

I agree. I am just looking for large differences so I am hoping it might be ok.

> Alternatively, have you considered using "housekeeping" or control genes?  These should be constant across arrays, experiments etc (if you believe in them) and so could provide a good normalisation factor.

Does anyone know if affy has control probes that are consistent across platforms?

Kind regards and thanks,

Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University

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