Re: [R] Quantile normalization and NA

From: Adaikalavan Ramasamy <ramasamy_at_cancer.org.uk>
Date: Sun 10 Jul 2005 - 22:31:49 EST

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@yahoo.com
> >
> > Raviabi
> >
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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sun Jul 10 22:38:42 2005

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