zero-score regulon

Open wangjiawen2013 opened this issue 3 years ago • 3 comments

Hi, When I run clustering with sns.clustermap(), an error occurred: FloatingPointError: NaN dissimilarity value. It caused by an weired value in the auc matrix. Some regulons (such as Ppp2r3d(+)) auc score are zeros for all the cells ! What does that (zeros for all the genes) mean and how to solve the problem ?

Sep 05 '22 01:09 wangjiawen2013

I changed the label of this issue because it is likely that the error you encountered is not caused by a bug in the pyscenic code.

How many target genes do you have for these regulons with AUC value equal to 0 for all cells?

Best,

Seppe

Sep 05 '22 07:09 SeppeDeWinter

I find there are only three genes !

Sep 05 '22 09:09 wangjiawen2013

Three genes is probably too low to calculate the enrichment values using AUCell. You can consider excluding these regulons to be able to draw your heatmap.

Best,

Seppe

Sep 06 '22 06:09 SeppeDeWinter