[BioC] gcrma and other normalizations

Raffaele Calogero raffaele.calogero at unito.it
Wed Jun 2 07:09:13 CEST 2004

if a don't mistake the present implementation of gcrma uses directly the 
quantile normalization.
Is there any command to switch off the quantile normalization, or how 
can I modify the gcrma function to eliminate the quantile normalization?

Since I would like to see  the effect of other normalization procedures 
on gcrma, is it a risonable procedure to normalize the data first  and 
subsequently applying the gcrma intensity calculation, after having 
modified the function in orther to remove the quantile normalization?
data.invariant<-normalize(data, method="invariantset")
data.gcrma.inv<-gcrma(data) #


Prof. Raffaele A. Calogero
Genomics and Bioinformatics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705410
Lab.   ++39 0116705408
Fax    ++39 0119038639
e-fax  ++39 0112365410
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   www.bioinformatica.unito.it

More information about the Bioconductor mailing list