what's the method of log-normalized in celldex

[shangguandong1996]

Hi, Dear Developer I noticed that according to the celldex manual, the value of celldex is log-norm or something like TPM.

Each dataset contains a log-normalized expression matrix that is intended to be comparable to log-UMI counts from common single-cell protocols (Aran et al. 2019) or gene length-adjusted values from bulk datasets.

But I am wondering whehter you can tell me what's the methods behind the log-norm count. Because I also want to make a similar database but for Arabidopsis thaliana

Best wishes

Guandong Shang

[j-andrews7]

The expression values vary between datasets. Many of them were simple log2(counts +1) transformations, some were pulled from databases that provided them in a log-transformed scale. You can see the various scripts that were used to download and process the data here.

Regardless, to make your own, a simple log2 transformation of raw counts is likely appropriate.