[R] Quantile normalization and NA
ramasamy at cancer.org.uk
Sun Jul 10 14:31:49 CEST 2005
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.
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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