Normalize intensity data — cr_normalize • cellreportR

Applies a channel-wise normalization. The normalized channel values replace the original column in cells.

Usage

cr_normalize(
  experiment,
  channel,
  method = c("background", "control", "zscore", "robust_zscore", "quantile"),
  control_group = NULL,
  ...
)

Arguments

experiment: A cr_experiment.
channel: Channel column to normalize.
method: One of "background", "control", "zscore", "robust_zscore", "quantile".
control_group: For method = "control": the treatment name (in design$treatment) whose median / mean is used as reference.
...: Additional arguments passed to the underlying method.

Value

A modified cr_experiment.

Details

"background" subtracts per-well background via cr_background_subtract() (percentile method, 5th percentile).
"control" divides each cell's intensity by the median intensity of cells assigned to control_group, then takes the log2 ratio.
"zscore" applies a global Z-score across all cells.
"robust_zscore" uses the median and MAD.
"quantile" maps the per-well empirical distributions onto the global quantile distribution.

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 30)
cr_normalize(exp, channel = "marker_1", method = "robust_zscore")
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 2911 across 96 wells
#> • Channels: "DAPI", "marker_1", "marker_2", and "marker_3"
#> • Design: 6 treatment groups
#> • QC steps applied: 0
#> ℹ Metadata fields: project, sop, and normalization