[BioC] RMA, RefRMA questions

[Kuhn, Max]

James,

>From the presentation that I saw on refRMA (and the paper), the quantile
normalization process would coerce the distribution of the low-level
probe data to have the same shape as the "reference" data. In
GeneLogic's case, they used sets of biological samples from their large
data base to define this reference distribution. Assuming that the
reference distribution used is acceptable for your samples/problem, this
should remove many of the systematic effects that you may have in your
data.

After googling, it seems that the package is only available form the
authors at this time, so I can't be exact.

As I mentioned earlier today, I have similar code that I'd be willing to
share. It works very similar to the affy RMA functions.

Max

 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James
Anderson
Sent: Wednesday, March 07, 2007 3:10 PM
To: bioconductor
Subject: [BioC] RMA, RefRMA questions

Hi,

I roughly understand the issue of RMA and RefRMA. When using RefRMA, one
RMA model is generated first based on the samples from one lab. If some
additional arrays measured in a different lab needs to be normalized,
does RefRMA automatically take care of the systematic difference between
the two labs or except RefRMA, there are still some extra work needs to
be done to correct the systematic difference between the two labs?

Thanks,

James

 
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