User: sabrina.mcnew

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Posts by sabrina.mcnew

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Comment: A: Use intercept or not in model matrix for edgeR methylation analysis
... Thanks James and Mikhael for pointing me in the right direction. 1) I did have a significant error in my code: the "contrast" and "coef" arguments should have been in the glmLRT() function, not the glmFit() function. 2) I also went and downloaded the bisulfite sequencing of mouse oocyte data from ...
written 7 weeks ago by sabrina.mcnew0 • updated 7 weeks ago by Gordon Smyth38k
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Comment: C: Use intercept or not in model matrix for edgeR methylation analysis
... Thanks Mikhael: you're right, the first design is without intercept and the second is with intercept. Do you have any idea why the models give me such different results? ...
written 7 weeks ago by sabrina.mcnew0
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Use intercept or not in model matrix for edgeR methylation analysis
... Hi: I'm trying to identify differentially methylated CpGs between two different treatments. I've been following the edgeR vignette as well as the Chen et al. 2018 paper but am running into confusing results depending on how I code the model matrix. If I code the model matrix with an intercept (as ...
edger methylation R glm written 7 weeks ago by sabrina.mcnew0

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