On 02/28/2012 05:07 PM, Brent Pedersen wrote:
> Hi,
> is there an example in the docs that I'm missing of using
> PCA to remove batch effects?

If your final goal is classification then you might want to
exploit the batch effect information instead of removing
it. Here is a nice paper you might find interesting:

http://www.citeulike.org/user/emanueleolivetti/article/8451376

I am spending some time on this topic so if you are interested
in it and your problem fits that solution we could discuss more.

Best,

Emanuele

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