Microarray comparison analysis

Upon completion of single array analysis, comparisons can be made between samples hybridised to different GeneChips to determine whether changes in gene expression occur between the two sample sets. One chip is designated as the ‘experiment’ chip, this is compared against the other ‘baseline’ chip. After scaling and normalisation of the two chips, analysis is performed to compare differences in value between probe sets.

The use of two algorithm sets creates statistical significance metrics for each probe set. The first algorithm creates a ‘Change p-value’ and an associated ‘Change Call’. The other algorithm generates a Signal Log Ratio (SLR) call based upon a quantitative estimate of change in gene expression.