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Answer: limma Intercept vs No-intercept models completely changing DMR results?
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This part:
```
design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa)
colnames(design_intercept) <- c("AltSHP_LA","Al…
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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.
Also take a st…
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See `?results`, in particular the lfcThreshold argument.
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You already ran a temporal assay. Now you can compare each time point to the baseline.
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