[BioC] scaling normalization between groups

[James W. MacDonald]

Hi Karin,

Karin Lagesen wrote:
> Hello
> 
> I have four groups a 5 chips each, all Affymetrix chips. I would like
> to be able to normalize them separately (within-group) and then see
> the scaling factor between them.

Are you trying to scale-normalize your four AffyBatches, or are you 
trying to figure out what the scaling factor would be?

> 
> I have now got so far that I have four normalized affybatch objects.
> 
> 
>>class(mockbgnorm)
> 
> [1] "AffyBatch"
> attr(,"package")
> [1] "affy"
> 
> 
> and three more like this one.
> 
> I was reading the normalize.AffyBatch.constant docs, and I gather that
> if I can make an affybatch object containing for instance all of
> mockbgnorm and one chip from the set I am comparing with, I can do
> normalize.AffyBatch.constant with the comparison chip as the
> reference. However, I am stuck at making this affybatch object.
> 
> Can anyone give me any tips on how to best do this? Am I thinking
> correctly?

If you are trying to scale things I don't think you really need to mess 
around with making different AffyBatches. You can simply get the mean or 
median of the AffyBatch or chip you are trying to scale to and then use 
that to scale the AffyBatch you are trying to normalize.

Best,

Jim


> 
> Thanks,
> 
> Karin


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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