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Then, mapped markers were used to run the linkage model and the admixture model, to compare the results obtained using different models and markers and to test the robustness of the results.
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The significance was determined empirically, by running the linkage test on ten permuted datasets.
To enhance spatial analysis of those data being collected, the HDSS also runs the data linkage system that enables it to link health facility based information with vital events.
Also, the main analysis was repeated after re-running the randomisation parts of the linkage process.
Hence, we performed tests for linkage disequilibrium and ran the program Haploview 4.1 which showed that the genome of the bison is mainly a mosaic of haplotype blocks where strong linkage disequilibrium between SNPs is observed (see please the last paragraph on page 5 and please see fig. 1, 2 and 3 where the blocks are shown graphically).
"If there is a linkage," said the president, "I personally believe it actually runs the other way.
It also runs the risk of identifying too many associated SNPs as a result of linkage disequilibrium or evolutionarily induced dependencies.
Recent literature (Birnbaum et al., 2009; Firoz et al., 2009; Kathiresan et al., 2009) reports several gene-disease associations that are not currently in OMIM but which were uncovered by one of the tested methods when run without using linkage intervals.
Finally, we performed a run in which the linkage preference was left ambiguous by defining a linkage restraint including both K48 and K63.
Hierarchical clustering was run with single linkage as arguments and the obtained dendrogram was then split into 9 clusters (Fig S4H).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com