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Hi, Sorry, I must have missed this. It may be a bit belated now but...
Jack |
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Hi Jack
I've been loving SCPA and the extra power and resolution it brings to single cell pathway analysis. I'm a young student using it for my master thesis on methotrexate pharmacodynamics in psoriatic arthritis, and it has helped me find some really interesting stuff. During this process though, I've been wondering about a few things:
Do you have any in vitro validation studies I could use for Q-value interpretation, and for reference?
What do you think about interpreting FC values independently of Q-value? I know these two have a natural relation in some fashion, but what would you say about a pathway that has a Q-value of 1.8 but a FC of 5 for example? Is there a 'hard stop' for Q-values where you discard a pathway and it's FC?
Also, do you have experience running the same dataset on different gene sets, and how do you feel this generally affects Q-values?
Kind regards and thank you in advance!
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