highly correlated hidden factors
I have a matrix of ATAC-Seq counts using imputation. I called hidden factors then using PEER bayesian method. The problem is all PEER factors are highly correlated like spearman correlation > 0.9. Does anyone has the feeling why it is happening?
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Angli Xue •
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Hi, have you solved this problem? I met the similar situation and trying to find out why.
use scale function in R to properly normalize the input matrix before calling PEERs and the problem of correlation will go away
Could I ask what is your sample size? I found that the correlation is still there when the sample size is ~30.