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Answer: ROAST compare results with complex design
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You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
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Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix:
```
> targets
ID Name phase G…
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I would like to clarify whether the command
`res <- results(dds, name = "phaseLP.conditionTreated")`
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Not sure I understand. You ask how to do something and then show how one would do so.
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Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
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