[BioC] NORMALIZATION OF AFFYMETRIX CHIPS DATA

[Rafael A. Irizarry]

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.
> > > 
> > > _______________________________________________
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> > > Bioconductor at stat.math.ethz.ch
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> > > 
> > 
> 
> 
>