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LoessF Normalization

normalize_loessf.Rd

This function is a wrapper around limma::normalizeCyclicLoess() with method = "fast". Each column is simply normalized to a reference array, the reference array being the average of all the arrays. See this paper for more information. Also see limma::normalizeCyclicLoess().

Usage

normalize_loessf(x, by = NULL, ...)

# S3 method for class 'glyexp_experiment'
normalize_loessf(x, by = NULL, ...)

# S3 method for class 'matrix'
normalize_loessf(x, by = NULL, ...)

# Default S3 method
normalize_loessf(x, by = NULL, ...)

Arguments

x

Either a glyexp_experiment object or a matrix. If a matrix, rows should be variables and columns should be samples.

by

Either a column name in sample_info (string) or a factor/vector specifying group assignments for each sample. Optional. If provided, the normalization will be performed within each group.

...

Additional arguments to pass to limma::normalizeCyclicLoess().

Value

Returns the same type as the input. If x is a glyexp_experiment, returns a glyexp_experiment with normalized expression matrix. If x is a matrix, returns a normalized matrix.