Method for determining biological expression levels by linear programming

A computer-implemented method for determining, for a biological sample, a vector of expression levels, each expression level representing a quantity of a target, of a corresponding set of biological targets, that is present in the biological sample, the method comprising:

• obtaining a matrix of signal values P corresponding to the set of biological targets;
• obtaining a vector of lower signal values L and a vector of higher signal values H corresponding to the sample, each element of L being less than or equal to a respective element of H;
• determining a vector E, a vector s, and a vector t, that minimize a total sum of all elements of s and t, and satisfy constraints s≧L−PE and t≧PE−H, wherein the elements of the vectors E, s, and t are nonnegative real numbers;
• and
• outputting the vector E determined in the determining step as the vector of expression levels.

A computer program product comprising a computer storage medium configured to store plural computer program instructions which, when executed by a computer, causes the computer to determine, for a biological sample, a vector of expression levels, each expression level representing a quantity of a target, of a corresponding set of biological targets, that is present in the biological sample, by performing plural steps comprising:

• obtaining a matrix of signal values P corresponding to the set of biological targets;
• obtaining a vector of signal values A corresponding to the biological sample;
• determining a vector E, a vector s, and a vector t that minimize a total sum of all elements of s and t, and satisfy a constraint PE+s−t=A, wherein the elements of the vectors E, s, and t are nonnegative real numbers;
• and
• outputting the vector E determined in the determining step as the vector of expression levels.