## User: ri.lars

ri.lars •

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**40**- Status:
- New User
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- Last seen:
- 10 months, 1 week ago
- Joined:
- 5 years ago
- Email:
- r******@gmail.com

#### Posts by ri.lars

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... 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.
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written 11 months ago by
ri.lars •

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... 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 11 months ago by
ri.lars •

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... 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 ...

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... 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.
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written 18 months ago by
ri.lars •

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... 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 18 months ago by
ri.lars •

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... 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 ...

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... 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 ...

#### Latest awards to ri.lars

Popular Question
4.4 years ago,
created a question with more than 1,000 views.
For Confidence intervals on edgeR logFC

Student
5.1 years ago,
asked a question with at least 3 up-votes.
For Confidence intervals on edgeR logFC

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