User: rasmus.agren

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Posts by rasmus.agren

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Comment: C: Paired design in limma
... Great, thanks! I didn't know that `D:T` would retain all levels. That's useful so you don't have to fiddle with factor level order. ...
written 7 months ago by rasmus.agren0
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Paired design in limma
... Hi, I wonder if someone could double check that this design is fine. I have a design with paired samples and I'd like to test for the effect of the treatment and the interaction between treatment and group. This is the experiment: Overweight and normal patients are investigated for their response ...
limma paired written 7 months ago by rasmus.agren0 • updated 7 months ago by Aaron Lun25k
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Comment: C: Limma design/contrast correct?
... Thanks! I answered too quickly and forgot that the example model I posted here didn't include an interaction term. Now I understand your point. My initial question was badly formulated because the model didn't answer the list of "questions we'd like to answer". That's because the purpose of the post ...
written 8 months ago by rasmus.agren0
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Comment: C: Limma design/contrast correct?
... Thanks a lot for such an exhaustive answer! I will need some time to digest this, but I wonder if you could explain what you mean with "This approach avoids making additive assumptions about how the sex/drug/intervention factors interact with each other.". I actually already use your way of formulat ...
written 8 months ago by rasmus.agren0
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Comment: C: Limma design/contrast correct?
... Sure, it would look something like this (skipping all confounding variables other than batch). `patient_id` would be the random factor that is called `pData(es)$Subject` in my initial post. ``` # 5 batches, 4 subjects per batch, 2 samples per subject batch <- rep(1:5, each = 8) # First 3 batche ...
written 8 months ago by rasmus.agren0
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Limma design/contrast correct?
... Hi, I wonder if the design/contrast I'm using in Limma is the best one for my experiment. In particular, I'm not sure of how `duplicateCorrelation` works here. I though I'd post the design here and hopefully someone can give me some hints. The research question is quite straight forward, but there ...
microarray limma paired design mixed model written 8 months ago by rasmus.agren0 • updated 8 months ago by Aaron Lun25k

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