[BioC] NORMALIZATION OF AFFYMETRIX CHIPS DATA

Stephen Nyangoma S.Nyangoma at cs.rug.nl
Mon Aug 18 22:37:03 MEST 2003


Thanks for this info. I will try it ou.

Regards. Stephen.


On Mon, 2003-08-18 at 23:33, Rafael A. Irizarry wrote:
> if you are using affy, the typical thing to do is normalize the probe
> level data. if you have probe level data in an AffyBatch object you can
> use the normalize method and decide on the normalization approach via the
> "method" argument.
> the vignetts for the affy package have much more info. i dont think
> normalize will work on matrix.
> 
> the different methods have "engine" functions that work on matrices so if
> you want to normalize data on a matrix you can do this as well but you
> need to call functions other than "normalize", for example
> normalize.quantiles, normalize.qsplines. in general normalize.methodname. 
> look at the help file for normalize.
> 
> notice that by default the functions  mas5, rma, and justRMA do the
> normalization as part as the reduction of probe level data to expression
> summaries.
> 
> -r
> 
> On Mon, 18 Aug 2003, Stephen Nyangoma wrote:
> 
> > Hi Rafael,
> > Sorry, I have just used
> > normalize.quantiles(mydata) and seems to have worked (given me
> > something). But wanted to use the 
> > normalize() object. Does this work differently? Where can I get more
> > information on how each normalization method works. My aim is to use a
> > variety of methods to explore this data set.
> > 
> > I am using library(affy).
> > 
> > Regards. Stephen.
> > 
> > 
> > 
> > On Mon, 2003-08-18 at 22:56, Rafael A. Irizarry wrote:
> > > what kind of object is Data8pm? normalize doesnt work on any R object.
> > > plus different types of ata are nornalized differentily. 
> > > 
> > > 
> > > On Mon, 18 Aug 2003, Stephen Nyangoma wrote:
> > > 
> > > > 
> > > > Hi All,
> > > > Am trying to normalize a data set and obtaining the following error
> > > > 
> > > > > load("Data8pm.Rdata")
> > > > > normalize(Data8pm)
> > > > Error in normalize(Data8pm) : No direct or inherited method for function
> > > > "normalize" for this call
> > > > >
> > > > 
> > > > Can some one please, advise on the mistake I am making?
> > > > 
> > > > Thanks for your help.
> > > > 
> > > > Stephen.
> > > > 
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor at stat.math.ethz.ch
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> > > > 
> > > 
> > 
> > 
> >
> 
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