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Reverse Median Normalization from Study Samples

Source: R/reverseMedianNormalize.R
reverseMedianNormalize.Rd

Reverses median normalization (including ANML) that was previously applied to study samples (SampleType == "Sample"). This function is designed to work with standard SomaScan deliverable ADAT files where study samples have undergone median normalization as the final processing step.

This function validates that:

  1. Study samples have a median normalization step applied

  2. The normalization was the last transformation applied to study samples

  3. The correct reversal method is applied based on the normalization type

Usage

reverseMedianNormalize(adat, verbose = TRUE)

Arguments

adat

A soma_adat object with study samples that have been median normalized

verbose

Logical. Should progress messages be printed? Default is TRUE.

Value

A soma_adat object with median normalization reversed for study samples. QC, Calibrator, and Buffer samples retain their original normalization. The ProcessSteps header is updated to reflect the reversal operation, and median normalization-specific metadata fields are cleared.

Use Cases

  • Converting from normalized ADAT to unnormalized ADAT for custom normalization

  • Preparing normalized delivery data for use with medianNormalize() function

  • Backing out normalization to apply different normalization strategies

Data Requirements

  • ADAT file with study samples (SampleType == "Sample") that have been median normalized (either standard median normalization or ANML)

  • Intact header metadata with ProcessSteps field indicating the normalization history

  • Median normalization must be the last processing step applied to study samples

Examples

if (FALSE) { # \dontrun{
# Reverse normalization from a delivered ADAT file
normalized_adat <- read_adat("normalized_study_data.adat")
unnormalized_adat <- reverseMedianNormalize(normalized_adat)
} # }