Hi everyone

I like to do a PCA on an expression matrix . How could I (or can I even)
incorporate categorical factors into the mix. I've seen PCAs that allowed
for factors along with numerical measures, but am unsure how it would fit in
with probesets and celfiles (for eg.with plotPCA). For instance would this
make sense: A matrix such as

celfiles--->. . . . . . .
genes      .
 |              .
V              .
Factor1    . . . . . . . . . .
Factor2    . . . . . . . .
Factor3    .. . . .. . .

Is this feasible?

The reason I ask this is that I like to see how much of and influence each
factor is making on each sample.

Thank you.

-
Regards,
Sherosha

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