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Figure 2 | BMC Bioinformatics

Figure 2

From: Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring

Figure 2

General statistics. In light grey, RawGeno datasets labelled with "RG" as prefix; in dark grey, GeneMapper datasets labelled with "GM" as prefix. A. Comparison of the frequency of the "present" allele (i.e. the occurrence of an amplicon within a bin) according to the bin size, in datasets scored with an increasing bin width using RawGeno. B. Pearson's correlation calculated between the automatically scored dataset and the manually scored one (R2_Manual). C. Partial constrained analysis results. This data mining technique allows the removal of the variation explained by the manually scored dataset in the automatically scored one. As a result, the residuals contain information that is specific to the automatically scored dataset. RES_Pop is a measure of the discrimination power of these residuals in identifying populations. We computed and tested Pearson's correlations between the residuals and a contrast matrix indicating the population origin of samples (Mantel test, 1000 permutations). Significance levels: * (p < 0.05), ** (p < 0.01) and *** (p < 0.001).

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BMC Bioinformatics

ISSN: 1471-2105

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