User: Jake

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Jake0
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Posts by Jake

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Job: Postdoctoral and other positions in bioinformatics, Vanderbilt University, Nashville, USA
... The Hughey Lab in the Department of Biomedical Informatics at Vanderbilt is looking for exceptional individuals to join the team. We're interested in people who are hard-working, creative, and eager to learn. Successful applicants will have the opportunity to shape the research directions and cultur ...
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Comment: C: Limma for differential expression in a time-course
... Yes, that's what I meant, thanks. ...
written 9 months 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 9 months 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 9 months 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 9 months 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 9 months ago by Jake0 • updated 9 months ago by Aaron Lun19k

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