I need to compare microarray data, where all of the "cases" were hybridized in one batch and all of the "controls" in another, so I have no way of removing this batch effect.

What would be the best strategy to detect differentially expressed genes (if at all possible)?

  • $\begingroup$ I'm not very experienced with microarray data, but I'd say tread carefully. You might be able to do some normalization using household genes, if at all, but even this is not a substitute for what should have be done in the first place. $\endgroup$ – Eekhoorn Oct 10 '13 at 20:03
  • $\begingroup$ Thanks for your input! Thats really the only possibility I've been considering myself. $\endgroup$ – slava Oct 10 '13 at 23:07

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