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A comparison of some adjustment techniques for use with quantitative spot data from two‐dimensional gels
Author(s) -
Kuick Rork D.,
Hanash Samir M.,
Chu Ernest H. Y.,
Strahler John R.
Publication year - 1987
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150080405
Subject(s) - spots , set (abstract data type) , biological system , data set , computer science , line (geometry) , chemistry , pattern recognition (psychology) , chromatography , analytical chemistry (journal) , mathematics , artificial intelligence , biology , geometry , programming language
Quantitative analysis of polypeptide differences among sets of identically prepared two‐dimensional polyacrylamide gels is facilitated by the use of mathematical transformations of the spot integrated intensity data for each gel in order to make comparisons. Such adjustments are needed because technical factors cause the stained polypeptide spots displayed on a particular gel to simultaneously appear darker or lighter than on another gel. We have compared three different adjustment schemes by applying each to the same set of data and testing to determine which gives smaller coefficients of variation for a large battery of spots. The adjustment that gave the best results is one based on regressing the spot integrated intensities of a standard gel versus each “target” gel and using the fitted line to transform the spot integrated intensities on the target gel. This adjustment is intuitive, easy to compute, and performed well regardless of whether the spots with large variability were included in the data or not.