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 > > [EMAIL PROTECTED] > > > > Raviabi > > > > ______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide! > > http://www.R-project.org/posting-guide.html > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
