Coffalyser.Net can format the probe ratios in the comparative analysis experiment explorer in several different ways. Depending on your preferences and setup, a different format might provide a better overview over your experimental results. 

The following conditional formats are available:

• Arbitrary: Probe ratios above the upper arbitrary border are coloured blue, while ratios below the lower arbitrary border are coloured red. Other probes are coloured based on the regions defined in the Coffalyser sheet.
• Gradient: Probe ratios below 1 are coloured increasingly red, while ratios above 1 are coloured increasingly blue. Normal ratios are displayed in black.
• HierarchicalPerSample: Probe ratios are coloured based on the lowest and highest ratios of the sample. The lowest ratios are the brightest red, while the highest ratios are the brightest blue. Intermediate ratios are displayed in yellow. This is useful to quickly identify the most extreme ratios in each sample.
• HierarchicalSampleGroups: Same as HierarchicalPerSample, except that the lowest and highest ratios of the sample group (e.g. samples, reference samples) are used. 
• HierarchicalAllSamples: Same as HierarchicalPerSample, except that the lowest and highest ratios of all samples are used (including reference and positive samples).
• ProbabilityScoresToReferenceSamples: Probe ratios are coloured based on a combination of whether or not the ratio crosses an arbitrary border and on the degree of overlap between the 95% confidence intervals of the probe in the sample as compared to the 95% confidence interval of the probe in the reference samples. This is the default conditional format. More information on the 95% confidence intervals can be found in the Reference Manual.
• ProbabilityScoresToAllSamples: Same as ProbabilityScoresToReferenceSamples, except that the 95% confidence interval of all samples with sample type sample is used in the comparison.

All formats except the Hierarchical formats colour the ratios of probes for which no signal was identified in bright yellow.

The conditional format of the grid in the comparative analysis experiment explorer can be changed as follows:

• Right-click in the grid.
• Select the desired format from the Conditional Format submenu.