User: ri.lars

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ri.lars40
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Posts by ri.lars

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Predict circadian expression with edgeR
... Great! That was exactly what I wanted. I tried using the model coefficients at first but I did not realise I needed to scale them so they were all off. ...
written 6 weeks ago by ri.lars40
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Comment: C: Predict circadian expression with edgeR
... Yes, that is what I was hoping to model - good to hear that it is correct. My question was more: "how do I use the estimated logFCs to calculate the expected CPMs at a time point I did not observe?" Today I realised I could calculate the expression as AveLogCPM + (logFC_control - logFC_KO) + time_e ...
written 6 weeks ago by ri.lars40
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Predict circadian expression with edgeR
... I have used edgeR and limoRhyde to predict differential expression in a circadian experiment. Below ZT_cos and ZT_sin is sin and cos transformations of the time variable as calculated by limoRhyde.  The model is of the form model.matrix(~ 0 + Genotype + Genotype:(ZT_cos + ZT_sin)) which results in ...
edger circadian rhythms limorhyde written 6 weeks ago by ri.lars40 • updated 6 weeks ago by Aaron Lun21k
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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 8 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 8 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 8 months ago by ri.lars40 • updated 8 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 4.2 years ago by ri.lars40 • updated 2.7 years ago by nwvidal0

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Popular Question 3.6 years ago, created a question with more than 1,000 views. For Confidence intervals on edgeR logFC
Student 4.2 years ago, asked a question with at least 3 up-votes. For Confidence intervals on edgeR logFC

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