[BioC] rma on new samples

[Kuhn, Max]

There are a few ways to do this. The basic issue is that the RMA normalization and summarization steps use data across multiple chips.

There is a package called refRMA that normalizes to a pre-defined database of data generated by GeneLogic. See 

   http://www.biomedcentral.com/content/pdf/1471-2105-7-464.pdf

for more details.

I have approached the problem by keeping the background correction the same and then

  - normalize the PM values of new samples to a reference distribution defined by the training set PM values 
  - computing a trimmed mean to get the summary measure

I'm sure that others have done something similar too. 

I have code to do this (the normalization is based on some code from limma:::normalizeQuantiles). I will send you (or anyone else) the code in another email if you are interested.

I've looked at comparisons in performance in my approach, regular RMA and MAS5 and found that the two RMA methods are pretty similar and MAS5 did very poorly. This could have been due to my particular problem and data (I was using the Staph chip), so take that for what it's worth.

Max 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Malick.PAYE at eu.biomerieux.com
Sent: Monday, March 05, 2007 1:47 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] rma on new samples

hello,

I work for an invitro diagnostic company (www.biomerieux.com) and we are 
interested in classification of patients based on expression profile (we 
are working with affymetrix chips).

I built a classification model based on a training set and i have new 
samples and i want to make my new samples comparable with the training set 
in order to apply my built model.

We use RMA to compute expression measures.

If someone have a code to do this, it would be very greatful for me.

Ideally i want to extract rma parameters and apply them to my new samples, 
or if someone have a better idea.

Thanks in advance.

M.P

Malick Paye | bioMérieux | Biomathematician
Phone: (+33)4 78 87 70 97 | Fax: (+33)4 78 87 53 40
[Centre Cristophe Mérieux, 5 Rue des Berges, 38004 Cedex 01  Grenoble, 
France]


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