Hi all,

I'm a budding researcher learning edgeR primarily by reading through the official User's Guide. I'm analyzing an RNA-seq dataset with six samples, three in each of two groups. I found the User's Guide a bit cryptic as to whether I should use the classic edgeR approach (exactTest) or the GLM functionality (glmQLFTest). I understand the classic approach is useful for experiments with only a single factor, like mine, but the authors of the User's Guide often used the glm approach in examples even with a single factor. Any tips?

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We currently recommend glmQLFTest for all bulk RNA-seq experiments with replicates because it gives better error rate control than other approaches. It is just as easy to apply as the classic exactTest approach but provides lots more options. See for example

• edgeR: exactTest, glmFIt or glmQLFit approach?
• EdgeR glmLRT vs glmQLFTest