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akdess / CaSpER

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Running CaSpER without Recerence Normal samples? #64

Open lmasatti opened 3 years ago

lmasatti commented 3 years ago

Dear akdess,

I'm running CaSpER on my bulk samples of different patients before and after a treatment. Like you often mention in the paper of CaSpER, in many cases like in mine, there is no matching normal sample of data. Is there the possibility to run the analysis without having a normal (reference) sample? Or I necessarily need to use a generic normal reference sample of the tumor I am working with? Because I see in your CreateCasperObject function the parameter control.sample.ids without which it seems not being able to work. Is there the possibility to fix this issue without providing the normal samples? If yes how can I set the function?

Thank you so much, Laura

guttula91 commented 3 years ago

same error i got did you able to solve the issue

lmasatti commented 3 years ago

Actually, I didn't find a way to run it without normal samples, unfortunately.

meeshelle-f commented 2 years ago

Hi I'm looking at oocyte scSEQ data using CaSpER. Since there are no reference or control samples I just input that they all were control. CaSpER still worked! No TPR for my data though so I am not sure how well it worked, but it looks good so far!