Parameter Selection

[radio1988]

With scImpute, how can we select parameters for drop_thre and Kclusters? Should we always use the default? Thanks!

[Vivianstats]

Hello,

For drop_thre, I suggest that you start with 0.5 and in most cases, it works pretty well.

As for Kclusters, you can perform an initial clustering of the raw data, and hopefully, that gives you a vague idea of the approximate number of clusters in your data. A smaller Kclusters makes scImpute more conservative.

Best, Vivian

[radio1988]

Thanks for the explanation!