Batch correction in Post-Chronos datasets

Dear DepMap Team,

I am curious about the batch correction method used by DepMap on their post-Chronos datasets, given the availability of multiple batch correction pipelines as mentioned in ‘Integrated cross-study datasets of genetic dependencies in cancer’.

I am also interested in performing a spheroid screening in a cell line, and would like to compare my own post-Chronos dataset with post-Chronos dataset in DepMap. However, our time points are different. Is it still possible to make meaningful comparisons between the datasets after batch correction?

Thank you very much,


Hi Nicole,

The larger concern is usually library batch effects. If you’re doing a screen in a library other than Avana/Humagne/KY, there will be large reagent-based batch effects. The time batch effect is not too large unless your timepoint is very different (<14 days or > 26 days).

Either way, with only one model I would not attempt per-gene batch correction. There is no way to distinguish a batch effect from a genuine biological difference. What you could do that’s relatively simple is a quantile normalization, so at least the overall distribution of effects is the same in your model and DepMap.