Dear all,
considering some of the pipelines that are described in https://bioconductor.org/packages/release/workflows/html/simpleSingleCell.html, would you please let me know, how could I modify the clustering parameters ("the resolution") in order to increase/or to decrease the number of CLUSTERS ?
thanks a lot,
- bogdan
Hi Aaron, thanks a lot for the quick reply ! very much appreciate it !
If i may add an additional question, it is related to filtering of cells, and normalization, before performing the clustering :
you'd always recommend data FILTERING (of cells, and genes) before NORMALIZATION (and NOT a NORMALIZATION step before FILTERING), correct ? thanks a lot !
Yes, I would filter out low-quality cells before normalization. Note that
computeSumFactors()
will automatically filter out genes for you, so that's not necessary; other normalization methods (e.g., library size normalization, spike-in normalization) are robust to low-abundance genes so they don't care.it is great to have your comments; thank you, Aaron !