[BioC] Quantile normailization and NA

Ravi Murthy ravidmurthy at yahoo.com
Tue Jul 12 01:11:05 CEST 2005

 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
 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

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.
ravidmurthy at yahoo.com  



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