Look at the package chemometrics, it can certainly handle your number of 
variables (p > n is what that's called and it requires special considerations). 
 I don't recall about missing values.  The authors of that package also have a 
very helpful text.  Good Luck. Bryan

On Jul 14, 2013, at 10:50 PM, kiran subedi <keas...@gmail.com> wrote:

> Hi,
> I am a researcher in chemistry. I have to do pls-da for some of my samples.
> The number of variables for my sample is 4000 . The categorical variable
> has two classes. Some of the values are missing (cant find out).
> I s there any package for R (or any illustration that would be helpful) to
> perform PLS-DA in R by ignoring the missing values.
> 
> 
> Thank you
> kiran
> 
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> 
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