You might be able to salvage some of the biology, depending on the
microarray that you used. If there are enough control probes on the array,
you could use something like Surrogate Variable Analysis on the control
probe values. However, do look into the types of control probes being used
(they don't just have to be negative control probes). The idea would be
that some portion of the differences across samples at these probes could
capture some of the batch effect (given you wouldn't expect the experiment
condition to be correlated with the control probe values). Then you could
adjust for the surrogate variables generated by these control probes in
your analysis of the regular probes.

-Andrew

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