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Note, that all project-related information, such as normalization, can be found on your REDFIN start page, by clicking on the info "i" icon next to each project.

The normalization is based on the gel-to-gel pair match relations and works under the assumption that the median protein between each gel pair is un-regulated.

The algorithm computes a normalization factor for each gel as follows, and uses it to normalize the spot volumes in that gel:

1. All matched spots between two gels are extracted and the top 50% matches, based on the spot volumes, are kept.
2. A spot volume ratio is calculated between each retained spot pair match. A pair-wise normalization factor between the gels is computed by taking the median of these ratios. This ensures robustness and accuracy even if the project contains up to 50% regulated spot volumes.
3. Each gel normalization factor is computed by optimizing an over-determined equation system, resulting from the pair wise normalization factors.
4. Finally, the spot volumes in each gel are multiplied with the corresponding gel normalization factor.

If there exist two gels without matches among themselves, the normalization algorithm above will not be used. Instead the following normalization algorithm will be used for all gels:

1. For each gel the sum of all spot volumes is calculated.
2. For each spot in each gel a normalized spot volume is calculated as: normalized spot volume = 10^6 * original spot volume / sum of all spot volumes

Hence for all gels the sum of all normalized spot volumes will be 10^6.