[BioC] GSE normalization

[Tan, Ruimin]

Hi Weiwei and steve,

Go to this link: http://www.biostat.harvard.edu/~wjohnson/ComBat/. I
tested this program, it worked fine for me. I don't have time to go
through this paper, but it maybe give you some idea.

Ruimin

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Weiwei Shi
Sent: Friday, June 22, 2007 10:05 AM
To: Stephen Taylor
Cc: Bioconductor
Subject: Re: [BioC] GSE normalization

hi, Steve:

if you look at my previous question, it has been suggested that pooling
data might not be a good solution.

-w

On 6/22/07, Stephen Taylor <staylor at molbiol.ox.ac.uk> wrote:
> Hi,
>
> > 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.
> >
>
> Someone has just advised me (off list) that the SOFT files can't be 
> analysed using rma since the data is at the gene level. So I guess 
> downloading the CEL files is the best approach...
>
> Ultimately I would like to incorporate other platform(s) as well, 
> though I realise this has many problems. Another set of data I have is

> from Functional ID v2.0 Array 1 from Rosetta, which I am not familiar
with.
> Does anyone know what is the best normalisation procedure for this 
> type of data?
>
> I agree with Weiwei though it would be useful to find out what is an 
> appropriate methodology. I have had a brief look around and seen a 
> bioconductor package called MergeMaid. Has anyone had any experience 
> with this or can recommend something else?
>
> Thanks again,
>
> Steve
>
> > HTH,
> >
> > Weiwei
> >
> > 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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> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
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> >>
> >
> >
>
>


--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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