Summary
Objectives:
We characterize typical problems encountered in microarray image analysis and present
algorithmic approaches dealing with background estimation, spot identification and
intensity extraction. Validation of the quality of resulting measurements is discussed.
Methods:
We describe sources for errors in microarray images and present algorithms that have
been specifically developed to deal with such experimental imperfections.
Results:
For the image analysis of hybridization experiments, discriminating spot regions
from a background is the most critical step. Spot shape detection algorithms, intensity
histogram methods and hybrid approaches have been proposed. The correctness of final
intensity estimates is difficult to verify. Nevertheless, the application of sophisticated
algorithms provides a significant reduction of the possible information loss.
Conclusions:
The initial analysis step for array hybridization experiments is the estimation of
expression intensities. The quality of this process is crucial for the validity of
interpretations from subsequent analysis steps.
Keywords
Microarray image analysis - spot identification - intensity extraction - validation
procedures
