This tutorial illustrates how to calculate a Principal Components Analysis (PCA) and a Multi Dimensional Scaling (MDS) (sometimes also called Principal Coordinates Analysis (PCoA)) on a fingerprint data set and how to change the layout of the obtained plots.
Any type of data that can be translated into a densitometric curve is considered a fingerprint type in the BIONUMERICS and GelCompar II software. This includes commonly used genotyping methods employing agarose or polyacrylamide slab gel electrophoresis (PFGE, rep-PCR, RAPD, PCR-DGGE, etc.), in which case the data are usually imported as two-dimensional gel images (bitmaps). Another major group consists of capillary electrophoresis profiles such as AFLP, ARISA, T-RFLP, etc. Here, the raw electropherograms generated by an automated sequencer (genetic analyzer) or derived peak table text files can be imported. Finally, any other profile (generated e.g. by gas chromatography, HPLC or spectrophotometry) that can be seen as peaks or bands, can be analyzed as a fingerprint.
The DemoBase Connected demonstration database. This database is used in several tutorials.
Note that the downloaded database backup file (.bnbk) can be restored via the Restore database... functionality in the BIONUMERICS startup screen.