A normalization commonly used with intensity-based data (CODEX, CyCIF, IMC). It effectively handles a wide dynamic range and zero/near-zero values while preserving the relative differences between signals of different intensities.
$$\LARGE x'_{i,j} = \operatorname{arcsinh}\left({\frac{x_{i,j}}{c}}\right) $$
Where:
(\(x_{i,j}\)) is the raw intensity for feature \(i\) in sample \(j\)
(\(x'_{i,j}\)) is the normalized intensity for feature \(i\) in sample \(j\)
(\(c\)) is a cofactor that determines the degree of transformation
The cofactor \(c\) prevents over-amplification of small values and allows better differentiation of signals at different intensities.
Common values to use are:
c = 5 for fluorescence imaging-based proteomics (CODEX, CyCIF)
c = 1 or 5 for mass-cytometry-based imaging (IMC).
c | numeric (default = 5). Expressed as \(c\) in the above formula. |
Other normalization parameters:
norm_default,
norm_l2,
norm_library,
norm_log,
norm_osmfish,
norm_pearson,
norm_quantile,
norm_tfidf