[R] Quantile normalization and NA

Uwe Ligges ligges at statistik.uni-dortmund.de
Sun Jul 10 12:34:41 CEST 2005

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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