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SofieVG / FlowSOM

Using self-organizing maps for visualization and interpretation of cytometry data
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Using `importance` argument for SOM mapping? #61

Closed mdmanurung closed 1 year ago

mdmanurung commented 1 year ago

Hello,

I saw that FlowSOM has an argument to weight markers with the importance argument, in which the expression values were multiplied by whatever factor that the user put in. However, as far as I know, this argument is not used frequently. I naively thought that it makes sense to weight a marker differently so that it drive the clustering, especially when considering prior knowledge. Do you have any thoughts that you can share about this or should I just stay away?

Cheers, Mikhael

SofieVG commented 1 year ago

Dear Mikhael,

While it might indeed be helpful in specific cases, in my experience it is often quite difficult to put exact numerical weight values based on more abstract prior knowledge. Therefore, I don't use it often, but if it would be helpful in your case certainly feel free to explore it!

Kind regards, Sofie

mdmanurung commented 1 year ago

Thank you for sharing your thoughts!