Expression data normalization

flatironinstitute / inferelator

Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.

BSD 2-Clause "Simplified" License

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Expression data normalization #24

Closed vvelasqz closed 1 year ago

vvelasqz commented 4 years ago

Do you recommend any type of normalization for expression RNASeq counts or should it work with raw data?

asistradition commented 4 years ago

I would suggest that you use either UMI-based counts or TPM. You may get a modest improvement if you add a transformation. Log2 pseudocount, the variance-stabilizing transformation from DESeq2, or a freeman-tukey transform would be good options.