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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler.
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1.
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
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Thank you Pierre! I'll try this out with my full data set.
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