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)?

Migration from GelCompar II to BioNumerics

Can I start with GelCompar II and upgrade to BioNumerics later?

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