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Answer: limma Intercept vs No-intercept models completely changing DMR results?
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I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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This part:
```
design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa)
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Thank you Tim, this is a great help in getting me started!
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Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first.
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