Hi, I am new to R, I am doing quantile normalization with a data consisting of a matix 384 X 124. While using "normailze.quantiles" I find that it introduces 'NA' into some of the cells, where we should expect a numerical value, can someone help me to overcome this problem ? The matrix consists of 62 plates in repliccate, and quantile normailization is done for the data from replicates (colomn 1,2) using normailze.quantiles function from 'affy' package resulting in data output as g1 >g1 <- normalize.quantiles(exprs(MSExpr[,1:2])) etc., uptp g62 This command works well for smaller series of data, but while using for a larger data matrix, it introduces "NA" in the place where it is suppose to geneerate data . It doesn't make any sense because elsewhere in the colomn consisting of similar values it computes properly. In addition, if I continue to perform median normailzation of the quantlies, the function fails to give any output, execept for those colomns which does not have any "NA". I cannot get rid of interference of NA in median normalization by using any of NA related functions. I am using R in MAC based platform for this analysis. Please suggest me some way to avoid 'NA' related computation problem. Ravi ravidmurthy at hotmail.com _________________________________________________________________ Don’t just search. Find. Check out the new MSN Search!

If your data initially has NAs then it is quite probable that normalize.quantiles() would introduce additional NA (or more likely turn the entire matrix into NA) since it does not make special allowances for NA values. I think the normalizeQuantiles() function in the limma package handles NA's more appropriately. Ben On Thu, 2005-07-21 at 13:59 -0500, Ravi Murthy wrote: > Hi, > > I am new to R, > I am doing quantile normalization with a data > consisting of a matix 384 X 124. > > While using "normailze.quantiles" I find that it introduces 'NA' into some > of the > cells, where we should expect a numerical value, can someone help me to > overcome this problem ? > > The matrix consists of 62 plates in repliccate, and > quantile normailization is done for the data from replicates (colomn 1,2) > using normailze.quantiles function from 'affy' package resulting in data > output as g1 > > >g1 <- normalize.quantiles(exprs(MSExpr[,1:2])) > etc., uptp g62 > > This command works well for smaller series of data, but > while using for a larger data matrix, it introduces "NA" in the place where > it is suppose to geneerate data . It doesn't make any > sense because elsewhere in the colomn consisting of similar values it > computes properly. > > In addition, if I continue to perform median > normailzation of the quantlies, the function fails to > give any output, execept for those colomns which does > not have any "NA". I cannot get rid of interference of NA in median > normalization by using any of NA related functions. > > I am using R in MAC based platform for this analysis. > > Please suggest me some way to avoid 'NA' related computation problem. > Ravi > ravidmurthy at hotmail.com > > _________________________________________________________________ > Dont just search. Find. Check out the new MSN Search! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor