[BioC] GSE normalization

Weiwei Shi helprhelp at gmail.com
Fri Jun 22 17:03:39 CEST 2007

hi, Steve:

I posted a similiar question as you yesterday and my situation is a
little bit different from you:
I have two ideas and one of them is to evaluae the variance across
sites so normalization should not be done for that purpose; but my
second idea needs the normalization, and my way of doing that is pool
the CEL files in one directory and run justGCRMA or whatever on them.
I am working on this approach now. Maybe we (or anyone interested in
this) could share the experience.



On 6/22/07, Steve Taylor <staylor at molbiol.ox.ac.uk> wrote:
> Hi,
> I have created 3 separate GSE Objects, read from SOFT format files using GeoQuery. I would like to normalise across experiments using rma. What's the best way to merge the data and then normalise?
> Ultimately I want to analyse these using limma.
> Thanks for any help,
> Steve
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Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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