R help - Jan 2013 - R package for normalizing microarray with few samples

I have only *two* datasets from normal and cancer samples.

              Cancer    Normal
--------------------------------------
mRNA1      30        49
mRNA2     199        200
...                 ...       ...
mRNA1000   13        40


Each samples contain several thousan mRNA microarray expressions.
The final aim is to identify mRNAs that are significantly
down/upregulated.

What is the best R package we can use for this?

- G.V.

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