search

carmonalab / UCell

Gene set scoring for single-cell data
GNU General Public License v3.0
132 stars 16 forks source link

Comparability of gene set of different sizes #1

Closed kvittingseerup closed 3 years ago

kvittingseerup commented 3 years ago

Hi

I'm very interested in UCell - it looks very promising.

Are the scores derived from different gene sets of different sizes comparable? (e.g. can I interpret which of two gene sets are more active / expressed?).

Btw to convince more people you could also compare to ssGSEA.

Cheers Kristoffer

mass-a commented 3 years ago

Thanks for your comments!

UCell scores are normalized by the size of the gene set (see the formula for the scores in the preprint), so they should be comparable regardless of gene set size. You can test this by evaluating the UCell scores for a large gene set and compare it to random subsets of the gene set of different sizes.

We made UCell to score and annotate individual cells, but it is true that global statistics could also be calculated to perform similar analyses to single sample GSEA.

Cheers and thanks.

kvittingseerup commented 3 years ago

Thanks for the quick response :-)