User: cadeans

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Posts by cadeans

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Getting up/down regulation info on DEG using edgeR
... Hi All, I've gone through and done all my contrasts for a rather large DE experiment using edgeR. I have logFC, logCPM, LR, PValue, and FDR for each of these contrasts but I can't figure out how to add a column that shows up/down regulation for each of my DEGs. I've tried extracting this informatio ...
edger differential gene expression written 3.8 years ago by cadeans0 • updated 3.8 years ago by Steve Lianoglou12k
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Comment: C: edgeR effects of design on testing main effects and interactions
... Thanks for your explanation Aaron. I'm afraid I'm still a little confused. Please bear with me. When I say a "main effect" of diet, what I essentially want to know is which genes are DEed across all diet treatments, regardless of stress (main effect of stress would be DE across stress treatments reg ...
written 3.9 years ago by cadeans0
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edgeR effects of design on testing main effects and interactions
... Hi all,  I am new to R scripting and bioinformatics in general. I'm using edgeR to run DE statistics on a project with 2 factors: diet (consisting of 4 diets: 12, 24, 30 ,39) and stress (consisting of 5 stressors: C, L, H, B, LB). I have 4 replicates per treatment (80 samples in total). I would lik ...
edger glmlrt() glmfit written 3.9 years ago by cadeans0 • updated 3.9 years ago by Aaron Lun25k

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For edgeR effects of design on testing main effects and interactions

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