Spectrum Count Normalization in Scaffold

Our protein normalization entails averaging the spectrum counts for all of the biosamples and then
multiplying the spectrum counts in each sample by the average divided by the individual sample’s sum.

For example:
 
Two Samples:  A and B
 
Each sample has three proteins:  One, Two and Three
 
Protein One has 12 spectra in Sample A and 8 spectra in sample B
 
Protein Two has 6 spectra in Sample A and 3 spectra in sample B
 
Protein Three has 4 spectra in Sample A and 3 spectra in sample B
 
Scaffold would normalize these spectra as follows:
 
Sample A has 22 spectra
Sample B has 14 spectra
 
Average is 18
 
Scaffold would multiply all of the protein spectral counts in Sample A by (18/22) and all of the spectral
counts in Sample B by (18/14).
 
For example:  Protein One in Sample A would be 12x(18/22) and Protein One in Sample B would be
8x(18/14)

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