wiki:CalculatePeakMatrixScore

Export Feature Matrix

This module can be used to calculated the score on the Feature Matrix, this score is dependand on the performance of the workflow. Different workflows could result in different scores, the one with the highest score is the workflow most suitable to analyze this kind of data with.

Usage Example

Parameters

Option name Description
inputFile Select the Feature Matrix on which U want to calculated the score
mzrtList The list of features identified by retention time (in minutes) and m/z which are different between classes
formulaPvalue value for the p in the score function see article
formulaXvalue value for the x in the score function see article
rtMin feature's with this or higher retention time are included in the calculation for the score of the feature matrix (retention time in minutes)
rtMax feature's with this or lower retention time are included in the calculation for the score of the feature matrix (retention time in minutes)
mzMin feature's with this or higher m/z value are included in the calculation for the score of the feature matrix
rtWindow this is the maximum time difference from the spiked peak in the mzrtList to the processed data (retention time in minutes)
mzWindow this is the maximum difference in m/z between the spiked peak in the mzrtList and the feature in the processed data
lookForIsotopes true or false, when this is checked isotopes are added as true positive peaks
includeTheFirstIsotopeOnly true or false, when this is checked only one feature per spiked peak in the mzrtList is counted as a true positive peak
rtWindowIsotope maximum difference between the first isotope and the 2nd, 3th, 4th etc. in minutes
mzWindowIsotope maximum difference between the first isotope and the 2nd, 3th, 4th etc. in m/z units

Note:

  • when only lookForIsotopes is "true" and includeTheFirstIsotopeOnly is "false" the number of true positives can vary between the different programs, making the scores difficult to compare between different module combinations.
  • when only lookForIsotopes is "false" and includeTheFirstIsotopeOnly is "true" only the first isotope of a spiked in peak is selected as a true positive if present other isotopes of this "true positive" peak are counted as false positives effectively penalizing the presence of isotopic peaks.
  • when only lookForIsotopes is "true" and includeTheFirstIsotopeOnly is "true" only one isotope per spiked in peak is selected as a true positive and the other isotopes are not taken into account for the analysis of the feature matrix.

Recommended is using true for both settings so that the isotopes are ignored if present and the maximum number for true positives for the different workflows are equal.

Last modified 7 years ago Last modified on Feb 8, 2012, 11:12:22 AM