﻿ General | Page 3 | Applied Maths

# General

General questions

### Jeffrey's X coefficient

A doubt has risen concerning the Jeffrey's X coefficient. According to the formula (#matches / #bands at lane a + #matches / #bands at lane b), the maximum value should be 2 (or 200 when expressed as %). However, in the similarity matrices the maximum number is 100 (the same as the other coefficients). What I would like to have confirmed is that BioNumerics simply normalizes the Jeffrey's X results by dividing them by 2 to facilitate the comparison with other coefficients.

### Minimum spanning tree rounding up data

When calculating a Minimum Spanning Tree for a character data set, if I select Categorical for the coefficient, it seems that the program is rounding up the non-integer values. However, from the manual, it seems that only the Summed absolute distance option would induce the rounding up.

### Minimum spanning tree with missing data

How are missing data treated when calculating a Minimum Spanning Tree? Is it tolerated or used as a zero value?

### Multi-Dimensional Scaling

What exactly is Multi-Dimensional Scaling (MDS) doing? Is it using the similarity matrix generated by the cluster analysis or does it generate its own? What are the labels for the x, y, and z axis?

### Authentication method used

What is the authentication method used between BioNumerics and the BioNumerics Server?

### Normalized distances

When doing an identification against a library with calculation of normalized distances, not all unknowns have normalized distances calculated. How come?

### Jackknife analysis

Why do groups need to be defined and a dendrogram to be calculated prior to Jackknife analysis?

### Difference between network version and BioNumerics Server

What is the difference between the BioNumerics network version and the BioNumerics Server suite?

### Statistics book reference

What textbook can I refer to for Principal Components Analysis, Multi-Dimensional Scaling, Discriminant Analysis, and MANOVA as implemented in BioNumerics (GelCompar II)?