I am working on a project that utilizes some geomx data, and I have tried many different normalization methods. I am now trying out yours. My understanding is that I can model normalized expression with a linear mixed model for DE analysis. Can I use poisson threshold normalized data as the input data to a linear mixed model? I see that this package supports negative binomial linear mixed modeling for the counts, but could I use the normalized data with a custom function that uses lme4? Modeling with the assumption that the data is approximately normal speeds things up a lot.
Also, I am noticing that the poisson threshold normalized data contains negative values. Is this expected? Is the data z-score scaled? Typically, if log2(count+1) is performed, there should be no negative values. Am I missing something here?
Any help would be much appreciated. Thanks in advance for your time.
I am working on a project that utilizes some geomx data, and I have tried many different normalization methods. I am now trying out yours. My understanding is that I can model normalized expression with a linear mixed model for DE analysis. Can I use poisson threshold normalized data as the input data to a linear mixed model? I see that this package supports negative binomial linear mixed modeling for the counts, but could I use the normalized data with a custom function that uses
lme4? Modeling with the assumption that the data is approximately normal speeds things up a lot.Also, I am noticing that the poisson threshold normalized data contains negative values. Is this expected? Is the data z-score scaled? Typically, if log2(count+1) is performed, there should be no negative values. Am I missing something here?
Any help would be much appreciated. Thanks in advance for your time.