Hi, I am new to R, I am doing quantile normalization with a data consisting of a matix 384 X 124 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 ? The matrix consists of 62 plates in repliccate, and quantile normailization is done for 2 colomn data per replicate using normailze.quantiles function from 'affy' package. >g1 <- normalize.quantiles(exprs(MSExpr[,1:2])) etc., uptp g62 This command works well for smaller sets of data, but while using for a larger data set, it introduces "NA" in the place where it is suppose to geneerate data . It doesn't make any sense because for similar values in the data set it computes properly, it randomly intorduces "NA" at some places, where there is no chance to have a missing value. 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". Please tell me what's the problem here, I cannot get rid of NA using any of NA related functions. I am using R in MAC based platform for this analysis. Ravi ravidmurthy at yahoo.com Raviabi __________________________________ Stay connected, organized, and protected. Take the tour: