Skip to contents

Apply log2 Transformation to Expression Data

Source: R/log_transformation.R
log_trans.Rd

Checks whether the input data is already log-transformed; if not, applies a log2 transformation. This helps ensure comparability of expression values across datasets.

Usage

log_trans(data, pseudo = 1, ...)

# S3 method for class 'matrix'
log_trans(data, pseudo = 1, ...)

# S3 method for class 'ExpressionSet'
log_trans(data, pseudo = 1, ...)

Arguments

data

A matrix-like data object.

pseudo

A numeric value added before transformation to avoid taking log of zero. For example, log2(exprs + pseudo).

...

Additional arguments passed to methods.

Value

A matrix or an ExpressionSet with log2-transformed expression values.

Details

The function heuristically determines whether data has been log-transformed, following the methodology used in GEO2R. If not, it applies log2() with the specified pseudo offset.

References

NCBI GEO2R: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE1122