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Apply log10 transformation to expression data

Source: R/preprocessing.R
log_transform.Rd

This function applies a log10(x + 1) transformation to the expression data in an ExpressionSet. This transformation is commonly used to stabilize variance and make the data more suitable for downstream analysis.

Usage

log_transform(eset, verbose = TRUE)

Arguments

eset

An ExpressionSet object containing expression data.

verbose

Logical indicating whether to print progress messages and create density plots. Default is TRUE.

Value

An ExpressionSet object with log10-transformed expression data.

Examples

# Load example data and create ExpressionSet
expr_data <- load_example_expression_data()
meta_data <- load_example_metadata()
eset <- make_ExpressionSet(expr_data, meta_data)
#> ✓ ExpressionSet created successfully
#>   - Number of genes: 57010 
#>   - Number of samples: 24 


# Apply log transformation
log_eset <- log_transform(eset, verbose = TRUE)
#> ✓ Log transformation completed