Benchmarking different DESeq2 design models
I have RNA time-course data and am looking to benchmark two different DESeq2 models I want to use. One design models time as a categorical variable, while the other design models time as a continuous variable. I am wondering if anyone knows of any R packages or methods to compute values such as AUROC to compare these two models performance in detecting DEGs.
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To generate AUROC statistics requires both a set of defined true positives and true negatives to serve as the “ground truth” to compare model performance against. This is typically achieved via cross validations when developing models.
For an example from a related post see www.biostars.org/p/271616/#271616
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