CALIB

CALIB estimates absolute target expression levels for two-color microarray data within Bioconductor by using external control spikes to calibrate intensities instead of relying on log-ratios.

Key Features:

• Platform: Supports normalization of two-color microarray data.
• External control calibration: Uses external control measurements (spikes) to estimate an absolute target level for each gene and condition pair.
• Absolute quantification: Produces absolute expression level estimates rather than relative log-ratios.
• Physically motivated calibration model: Employs a calibration model that does not assume a specific distribution of gene expression divergence.
• Parameter and error estimation: Estimates model parameters and error distributions from external control spikes.

Scientific Applications:

• Normalization for two-color microarrays: Provides calibrated expression values to improve comparability across two-color microarray experiments.
• Differential expression analysis: Supplies absolute expression estimates useful for downstream detection of differentially expressed genes.
• Pathway analysis: Enables pathway-level interpretations based on calibrated absolute expression measurements.
• Biomarker discovery: Facilitates identification of biomarkers by providing absolute reference points for gene expression across conditions.

Methodology:

Fits a physically motivated calibration model that estimates model parameters and error distributions from external control spikes to compute absolute target levels per gene and condition, avoiding log-ratio based measures.