Hello

Thank you for developing this great tool. I have a very basic question.

I want to use makeExampleDESeqDataSet to simulate RNA-seq data using pilot data, to test the power of different sample sizes in an experiment with two treatments.

However, I am confused about how to input the parameters from my pilot data. Disclaimer - I am a biologist not a statistician. I have tried to understand the methods section of the DEseq2 paper, but unfortunately I still don't follow how to do this.

For example, from my pilot dataset I have the mean expression and mean dispersion; how do these relate to the input parameters of makeExampleDESeqDataSet? ie betaSD /interceptMean / dispMeanRel / sizeFactors. I plan to simulate the treatments separately at different sample sizes, and then calculate differential expression and cohen's D for each.

Thanks

Lily