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YuanTian1991 / ChAMP

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apply combat and refbase #23

Open SofyaMa opened 2 years ago

SofyaMa commented 2 years ago

Dear Yuan,

Is it possible to apply champ.runCombat() followed by champ.refbase()?

Thank you in advance!!

YuanTian1991 commented 2 years ago

I suggest you do champ.runComat() first, then champ.refbase().

SofyaMa commented 2 years ago

Dear YuanTian,

Thank you very much for your reply. I appreciate it and applied it the way you said. Could you explain, why you suggest to first correct for batch and afterwards for blood composition? I think, I would start for correction from bigger effects to smaller ones and thus the blood composition should be done first. However, I might have understood it completly wrong .. Thank you in advance!

YuanTian1991 commented 2 years ago

The batch correction should only correct the batch you specified, like Slides/Array, they are factors not related to biology, so in theory, after batch correction, the blood composition information should be able to be retained after batch correction, it should not influence the blood type detection.

But you raised a good question, I never do any simulation for this, would worth to check if there are significantly different result if we do them different order.