Functional protein microarrays differ in many respects from DNA or RNA microarrays. Unlike DNA microarrays, functional protein microarrays often aim to discover global interactions of a single probe (protein) in a single colour-channel, which results in a relatively small selection of specific proteins showing strong signals for a given sample. In this regard, we have designed a robust data pre-processing method to ensure that each reported signal intensity is highly accurate and significant.
Each replica spot on the array is subject to multiple threshold variables for quality control purposes. These quality control steps ensure replica spots from proteins showing high variance are flagged to report outliers.
Our normalisation step uses both quantile-based and total intensity-based methods which utilises common underlying distribution of control probes on the array to correct for any technical variance whilst conserving the biological differences between samples.
The biomarker discovery step implements protein-specific threshold calculated based on mean signal intensities from healthy controls, thus highlighting case specific responses.
Each step of data analysis pipeline maintains the quality of data to report only true positive signals.