[R] Quantile normalization and NA

[Adaikalavan Ramasamy]

I agree with Uwe on both points.

Have you checked if your inputs, i.e. exprs(MSExpr[ ,1:2]), contain
missing values to begin with ?

Out of curiosity are you trying to apply this method to two colour
arrays ? You might want to enquire the BioConductor mailing list about
the merits of doing this over standard techniques (i.e. LOESS
normalisation) as I do not think this is widely done.

Regards, Adai



On Sun, 2005-07-10 at 12:34 +0200, Uwe Ligges wrote:
> Ravi Murthy wrote:
> 
> > Hi,
> > I am new to R,
> > I am doing quantile normalization with a dat matix of
> > 384X124 and I find that while computing the quantile
> > normailzation it introduces 'NA' into some of the
> > cells, can someone help me to overcome this problem ?
> > 
> > 
> > This is the command that goes like upto g62 for 124
> > colomns
> > 
> > 
> >>g1 <- normalize.quantiles(exprs(MSExpr[,1:2]))
> 
> Do you mean the function normalize.quantiles() from package "affy" 
> (please always tell the package, if the function is not in base R)?
> It's more appropriate to ask on the Bioconductor mailing list if 
> Bioconductor packages are the subject of interest.
> 
> And you might want to give a simple, reproducible, but 
> non-bandwith-wasting example (perhaps by uploadiung data to some web 
> site) in order to make the Bioconductor folks able help you.
> 
> Uwe Ligges
> 
> > 
> > For a small set of data there is no problem, but for a
> > large set of data, it introduces "NA" in the place
> > where it is suppose to geneerate data .
> > 
> > Ravi
> > ravidmurthy at yahoo.com  
> > 
> > Raviabi
> > 
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