[BioC] NA and quantile normalization

Ravi Murthy ravidmurthy at hotmail.com
Thu Jul 21 20:59:59 CEST 2005


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.
ravidmurthy at hotmail.com

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