One usage of ssGSEA is to evaluate the abundance of multiple gene-sets in the same sample to figure out which gene set is more abundant.

For those purposes would it be possible to turn off the use of .filterFeatures. Or at least prevent .filterFeatures from removing features based on missing values?

Cheers Kristoffer

Hi, the internal function .filterFeatures() does not remove any feature (row in the input expression data matrix) when the parameter method="ssgsea".