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If your tools don't generate useful insights, then you are not using them right. A properly designed study, employing high-dimensional genomics data, can for sure generate mechanistic insights, not just correlations. It's all about your study design.

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Some tools will never give you useful insights because they have inherent limitations, or the model being studied doesn't lend itself to an informative study design. Results get published anyway. Which is fine. My point was that many high throughput studies do not materially contribute to the advancement of knowledge. This is entirely compatible with your point that well designed high throughput studies can contribute.

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