Which parameter controls the between-replicate variance in the simulation code

[mingyudu]

Hi,

Can you tell me which parameter in the function 'splatSimulateGroups' controls the between-replicate variance in the simulation?

Thanks!

[skinnider]

See the Methods section

Simulations were performed using the ‘Splatter’ R package48, with simulation parameters estimated from the Kang et al. dataset5 using the ‘splatEstimate’ function. Populations of between 100 and 2,000 cells were simulated, with between 3 and 20 replicates per condition. DE of varying magni- tudes was simulated between replicates by varying the location parameter of the DE factor log-normal distribution (‘de.facLoc’) between 0 and 1, treating each replicate as its own group, and the total proportion of DE genes (‘de.prob’) set to 0.5. Then, half of the replicates were randomly assigned to an artificial ‘treatment’ condition and the remaining half to a ‘control’ condition, and DE analysis was performed between the treatment and control groups. Except where otherwise noted, plots show results from a simulated population of 500 cells, with three replicates per condition.