highly correlated hidden factors

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3.4 years ago

GK1610 ▴ 120

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?

ATAC-Seq data exploration analysis • 879 views

ADD COMMENT • link updated 2.6 years ago by Angli Xue • 0 • written 3.4 years ago by GK1610 ▴ 120

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Hi, have you solved this problem? I met the similar situation and trying to find out why.

ADD REPLY • link 2.8 years ago by Angli Xue • 0

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use scale function in R to properly normalize the input matrix before calling PEERs and the problem of correlation will go away

ADD REPLY • link 2.7 years ago by GK1610 ▴ 120

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Could I ask what is your sample size? I found that the correlation is still there when the sample size is ~30.

ADD REPLY • link 2.6 years ago by Angli Xue • 0

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