[BioC] microarray normalization

[Natalie Thorne]

Hi Alberto,

There has not been much in the literature (as you say) about normalizing
single-channel data.  I have been working on this, looking at combining
two-channel approaches that allow the recovery of logR, logG
single-channels (i.e pin-group lowess etc) plus approaches used for
affymetrix normalisation (i.e quantile normalisation).

In the following reference I wrote a small intro to the problem of
normalising single-channel data from two-colour cDNA microrarrays with
Jean.

Normalization for Two-color cDNA Microarray Data
Yee Hwa Yang and Natalie P. Thorne
IMS Lecture Notes -- Monograph Series, Volume 40, 2003
Science and Statistics: A Festschrift for Terry Speed
Editor: Darlene R. Goldstein


The main reason the rest of my work hasn't been published is that I am in
the last few months of finishing my PhD thesis (time issue!), but I plan
to publish soon after that.  My main focus is on the assessment of
proposed single-channel normalisation methods.

It sounds as though you may be using cDNA data which only has one colour.
I haven't had any experience with this kind of data, but I would recommend
you look at the quantile normalisation method (there is a routine in
the R Limma package library) and think/look carefully how it is doing.  We
find it works quite well.  If you do infact have two-colour data, try a
pin-group normalisation on the M-values, then quantile normalise across
slides the A-values.  Then take Mp and Aq and recontruct logR and logG
(pretty easy to figure out).

Hope this helps.

Natalie


On Fri, 8 Aug 2003, Alberto Labarga wrote:


> Dear Ms. Thorne,
> 
>  my name is Alberto Labarga, I work at university of Navarra, and I'm
> studying normalization methods for single-channel microarray data (not
> Affymetrix), becouse some people here are working with this technology, I
> saw in your home page that you are working in this subject, and Dr. Remiers
> also recommended to get in contact with you, could you give me some
> references for this subject or any hint on which would be the best approach?
> 
> thank you very much
> 
>  alberto
> 
> 
> ----- Original Message ----- 
> From: "Mark Reimers" <Mark.Reimers at biosci.ki.se>
> To: "Alberto Labarga" <alberto.labarga at unavarra.es>
> Cc: "Natalie Thorne" <thorne at wehi.edu.au>
> Sent: Friday, August 08, 2003 1:17 PM
> Subject: Re: microarray normalization
> 
> 
> > Hi Alberto,
> > for single-channel cDNA array I suggest you get in touch with Natalie
> >
> > Natalie Thorne <thorne at wehi.edu.au
> >
> > who has done a lot on this.
> >
> > regards
> >
> > Mark
> >
> > On Fri, 2003-08-08 at 12:36, Alberto Labarga wrote:
> > > Dear DR. Reimers,
> > >
> > >  I have seen that one of your research interest is normalization of
> > > single channel microarrays, I have seen that much of the literature is
> > > about two-color microarrays, but in our center (university of navarra,
> > > spain) we are doing single-channel (not Affymetrix), and we are trying
> > > to find a good normalization method,
> > >
> > >  could you give me some references for this subject?
> > > thank you very much
> > >
> > > alberto
> > -- 
> > Mark Reimers
> > Assistant Professor, Biosciences, and
> > Statistical Expert, Bioinformatics and Expression Analysis Facility,
> > Karolinska Institute
> > Stockholm
> >
> >
> 
> 
>