Scale of GRNBoost Results about scenic HOT 3 CLOSED

Hello,

I am not very familiar with the exact output of GRNBoost, but if I remember correctly, I think it provides a result similar to GENIE3 after converting the weightMatrix to linkList ( getLinkList(weightMatrix) ).

The scales of the weights might be different, but that should not matter too much, since they are mostly used to "rank" the TFs. You will only need to adjust the threshold in the next step of SCENIC, to create the gene-sets (co-expression modules) to analyse for motif enrichment (e.g. to get a similar number of genes. In any case, the gene-sets that are built only based on ranking, for example "top5 per gene"... should be quite consistent independently of the units...).

from scenic.

Hello,
indeed, the weights carry no other meaning than the ranking in the list of regulatory links.

from scenic.

Great, thanks for the clarification!

from scenic.