User: ri.lars

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ri.lars40
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Posts by ri.lars

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Comment: C: edgeR: Choice of reference group in nested model
... That is excellent, I find the construction of contrasts in R to be confusing and not all packages has the same flexibility as edgeR does so this will definitely help me in the future. ...
written 5 months ago by ri.lars40
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Comment: C: edgeR: Choice of reference group in nested model
... Thank you for the comprehensive explanation, that cleared things up quite a bit. What I am really interested in would be the log-fold change in the average of B1 and B2 over the average of A1 and A2. Can I design a contrast with my current model specification that would test this? Something like ((I ...
written 5 months ago by ri.lars40
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edgeR: Choice of reference group in nested model
... I have an experiment where each sample is measured multiple times and samples are nested within the experimental group. I have noticed that my choice of sample reference level seems to influence the results. Below is a minimal example to show what I mean: library(edgeR) counts <- matrix(c(6,2,6 ...
edger reference group nested design model.matrix written 5 months ago by ri.lars40 • updated 5 months ago by Aaron Lun21k
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Confidence intervals on edgeR logFC
... Is it possible to calculate a confidence interval on the log fold change reported in the output of edgeR? I suppose that knowing the number of reads in a gene and the tagwise dispersion one can find the total CV^2 for that gene, as 1/reads + dispersion, but where to go from there?  As an alternati ...
edger statistics confidence interval written 4.0 years ago by ri.lars40 • updated 2.5 years ago by nwvidal0

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For Confidence intervals on edgeR logFC
Student 4.0 years ago, asked a question with at least 3 up-votes. For Confidence intervals on edgeR logFC

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