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snap-stanford / SATURN

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The meaning of weights in macrogene? #59

Closed xuzhougeng closed 6 months ago

xuzhougeng commented 6 months ago

This is a very good work, and the results in my data are great.

I have some confusion about macrogene.

  1. The total weights of different macrogenes are different. Does this mean that the macrogene with higher weights has a greater effect？
  2. The weights of the same macrogene are different. Can they be filtered based on a threshold?
Yanay1 commented 6 months ago

Thanks!

  1. I would not interpret the macrogene weights in that manner. A high sum of weights to the macrogene could just mean there are many equally highly weighted genes to it.

  2. To interpret a macrogene we looked at some number of the top genes. Usually there is a dramatic drop off in the gene weights, one example for a cutoff was not looking at genes if the weight was below 0.5. But in some cases, all genes will have weights below 0.5 and you can only look at the top 3-10 or something.