User: Jenny G

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Jenny G0
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Posts by Jenny G

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Comment: C: Limma trend test with pre/post design and technical replicates
... There's a fair bit to consider here, I'll think it over. My concern is that I want to give some sort of measure of effect size, with a coherent description. Not so easy in this case, I think! I'll consider the ordinary factor approach too. I could compare each dose group to control, then filter out ...
written 10 months ago by Jenny G0
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Comment: C: Limma trend test with pre/post design and technical replicates
... Hi Aaron, Thanks again for your help. I'm struggling now with interpreting and explaining the FCs, with this design. I would like to present a table of results with p-values and FCs, then give a clear explanation of the analysis, and explain the results for one example (say, the top hit). I'd also ...
written 10 months ago by Jenny G0
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Comment: C: Limma trend test with pre/post design and technical replicates
... Thanks Aaron, I think I follow. A trend across within-patient changes sounds like what I want. I've done it this way and the results make sense. I've calculated percent change from baseline and plotted the hits, and they look good (e.g. effect sizes look right). Thank you for your help! ...
written 10 months ago by Jenny G0
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Comment: C: Limma trend test with pre/post design and technical replicates
... Hi Aaron, Thanks for your time and your help. My apologies for not explaining the experiment well, I've tried to clarify below. I have a few points/questions, if you have the time to help me. 1. Treatment is an ordered factor, so limma reports linear, quadratic and cubic effects (same as lm() does ...
written 10 months ago by Jenny G0
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Limma trend test with pre/post design and technical replicates
... Hi all, I have 4 dose groups, technical duplicates, and pre- and post-treatment data. I'm interested in detecting a linear trend across dose groups, adjusting for pre-treatment variability. I'm not certain how to set this up. Data is like this: patients <- data.frame(Patient = rep(c(1,2,3,4,5, ...
limma limma-trend written 11 months ago by Jenny G0 • updated 11 months ago by Aaron Lun24k

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