[BioC] How can I get the normalized data for each probe before summarizing in oligo package?

Laurent Gautier laurent at cbs.dtu.dk
Tue May 26 17:01:35 CEST 2009

Tae-Ho Lee wrote:
> Hi,
> I had successfully analyzed Nimblegen microarray data with oligo package,
> according to the document,
> http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/doc/oligoNimblegenExpression.pdf
> .
> However, I was not able to get normalized data for each probe since the
> 'rma' funcation returned expression data for each gene summarized via median
> polish.
> How can I get the normalized data for each probe before summarizing?
> Thanks for any help,
> Tae-Ho Lee

The general idea to do it is to extract your probe-level matrix with the 
accessor method "exprs()", then call the method "normalize.quantiles()" 
from the package "preprocessCore" (eventually after calling 
"rma.background.correct()" from the same package).

Note that you may have to extract the control probes out (others can 
correct me here, but I am remembering that oligo is removing controls 
prior to processing).


Laurent Gautier, Ph.D.
Building 301, CBS - Technical University of Denmark
DK-2800 Lyngby
Phone: +45 45 25 61 45     Fax: +45 45 93 15 85

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