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Repetitive regions are excluded from the Array.
SNPs within 15 bp of each other or insertion/deletions were excluded from the array.
Probes were excluded from the array design if they differed at fewer than 4 positions (for 12-mers) or 5 (for 13-mers) from previously selected probes.
The mRNA and the ESTs were then uploaded to the e-array portal, and again probes with BC scores of three and higher were excluded from the array.
The minor mastitis pathogen, coagulase negative staphylococcus spp., was found in three control quarters at 24 h after inoculation; specifically, two cows presented with increased SCC and these two quarters were excluded from the array analysis.
A large proportion of these were in the two obvious gaps which were excluded from the array design criteria due to known repeat content or sequences present multiple times in the genome (duplications).
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We have shown that the YRI maps are improved by the greatest margin due to the inclusion of common variation excluded from the array-based genotyping panel.
Our methods did not directly interrogate this aspect of DNA methylation biology since repetitive elements were excluded from the arrays to avoid cross-hybridization signals and because our method, like other restriction enzyme and enrichment based genome-wide DNA methylation assays, cannot robustly detect differential methylation in regions with very low CpG density [ 5, 6].
It may be because the mucosal part is basically retained in early GCs and because the mucosal precursor of an invasive component showed the lowest grade of atypism and was not excluded from the present array analyses.
In previous studies [ 32, 38, 39], a low level of DArT marker redundancy has been observed, however during the process of consolidating the most informative DArT clones in new arrays, the large majority of redundant markers are excluded from the final DArT array, and hence DArT marker redundancy should be minimised.
During this process redundant markers are excluded from the final genotyping array.
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