User: Jake

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Jake0
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Posts by Jake

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Comment: C: Limma for differential expression in a time-course
... Yes, that's what I meant, thanks. ...
written 6 days ago by Jake0
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Comment: C: Limma for differential expression in a time-course
... But limma does use all the samples from all the time-points in order to make that estimate, right? As part of the "extrapolation" you mentioned? I'm just trying to wrap my head around this. ...
written 7 days ago by Jake0
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Comment: C: Limma for differential expression in a time-course
... Sorry, I'm still confused. For detecting genes for scenario 1, I thought "model.matrix(~Group + X)" was an additive model, but you're saying coef=2 only looks at the first time-point. Do I need to use makeContrasts to look at the effect of group at each time-point? For randomly distributed time-poin ...
written 7 days ago by Jake0
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Comment: C: Limma for differential expression in a time-course
... Thanks for the quick and detailed response! A few questions: 1. I still care about distinguishing (1) genes for which the difference in expression between conditions is non-zero and constant over time from (2) genes for which the difference in expression between conditions changes as a function of ...
written 8 days ago by Jake0
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Limma for differential expression in a time-course
... I have a question related to example 9.6.2 in the Limma User's Guide. The example describes how to find genes whose behavior over time is different between two conditions, where each condition has a decent number of time-points. Reproduced here: X <- splines::ns(targets$Time, df=5) Group <- ...
limma differential expression multiple time points time-course written 10 days ago by Jake0 • updated 10 days ago by Aaron Lun16k

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