I have RNASeq count data from 42 different conditions, 5 repeats per condition for a total of 210 samples, and approximately 37,000 genes. DESeq freezes up at the estimateDispersions step unless I slice the data down to ~50 samples or so. Is it the case that the calculation time scales up in the extreme, or is it something about one or more of my samples causing the freeze? I have tried parallelising the step with 120 cores, but to no avail, and I feel like it's perhaps a crash rather than just a long calculation because I can't cancel it (though that's often the case in R so who knows).
Any advice appreciated.