[BioC] quantile normalization of one dataset to another

Benilton Carvalho bcarvalh at jhsph.edu
Tue May 22 16:26:49 CEST 2007

Assuming that the second dataset is quantile normalized and that its  
expression matrix is called "expression2", what you want to do is:

ref <- sort(expression2[,1])  ## if it is quantile normalized, every  
column has the same distribution
for (i in 1:ncol(expression1))
   expression1[order(expression1[,i]),i] <- ref


On May 22, 2007, at 10:17 AM, Daniel Brewer wrote:

> Hi,
> I have two different datasets which are both originally from the
> Affymetrix platform but now I only have the expression matrix.  Both
> datasets have an overall different distribution of expression.  What I
> would like to do is quantile normalisation on each of the  
> experiments in
> one dataset to the quantile curve of the other dataset i.e. I want to
> leave the second dataset untouched, but normalise the first to it.   
> ANy
> ideas how to do this?  I looked at normalize.quantiles but it does not
> appear to do what I want.
> Thanks
> Dan

Benilton Carvalho
PhD Candidate
Department of Biostatistics
Bloomberg School of Public Health
Johns Hopkins University
bcarvalh at jhsph.edu

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