I've simulated RNA abundance with wgsim. The simulation itself was error free. There is a single factor in my experiment that looks like:
A1 A2 A3 B1 B2 B3 R1_101 113 113 113 13 11 9 R1_102 247 246 246 12 12 14 R1_103 20835 20915 20788 9973 9955 9973
A1, A2, A3 are the simulated replicates for the first level. B1, B2 and B3 are the simulated replicated for the second level.
As expected, the reads counts for each level are very close because it was an error-free simulation. The purpose of the experiment is to compare it with cuffdiffs (another differential package) in detecting log-fold changes.
Unfortunately, I run into an error in DESq2:
Error in estimateDispersionsFit(object, fitType = fitType, quiet = quiet) : all gene-wise dispersion estimates are within 2 orders of magnitude
It looks like the package is unable to estimate a dispersion factor (most likely it's too small). However, I had no problem with cuffdiffs. Is there anything that I can do to make it work?