On Mon, Oct 18, 2010 at 4:42 AM, Hossain Nawaz <hmnawaz@gmail.com> wrote:

> I     Hi,
>
> I am using R and tried to normalize the data within each sample group using
> RMA. When I tried to import the all the normalized expression data as a
>  single text file and make a boxplot, it showed discrepancy among the
> sample
>
>  groups.  I tried to scale them or re-normalize them again, so that it can
> be
>  used for further analysis. Would you please help me out with this problem.
>
>
>
Hi, Hossain.

You should normalize all the samples together, not separately.  There are
numerous posts in the mailing list archives on how to accomplish this with
largish data sets.

Sean

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