Unable to understand the meaning in the workflow

[SerendipityCreate]

In the workflow, sample 2 showed high expression of the up-regulated differential genes in qulescence, while low expression of the down-regulated genes in qulescence. So, sample 2 should have a high qulescence score, but the final label was fast cycling.
How should this be explained?

[msecrier]

You will need to be more specific about which script your are specifically referring to. Overall, we calculate a continuous quiescence score and the cut-off for "high quiescence" is around 1.5, or 5 if we want to be more stringent. However, in the pan-cancer analysis we ended up using k-means clustering to assign samples to "highly quiescent" or "fast proliferating", and that could occasionally lead to a sample being mis-assigned to the group. That would only happen in a minority of cases though and would not affect the overall results.

If you want to apply this method to new samples, we recommend calculating the score and applying a cut-off of 1.5 (lenient) or 5 (stringent) for what is deemed to be a G0 arrested sample.