why ulm (and not mlm) for transription factor activities ? there must be some overlaps

[Sophon-0]

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[PauBadiaM]

Hi @Sophon-0,

The problem of mlm is that whenever there is high overlap between gene sets (regulons), results are unstable, and this is something that is quite common in gene regulatory networks. Specifically for PROGENy, since the gene sets were specifically built to be as orthogonal as possible, it is not a problem to run it with mlm. Therefore, whenever you suspect that your gene sets have high overlap (you can check this by running dc.check_corr) it is advisable to use ulm. For more information check this reply.