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Aberrant signals including 4 or more adjacent probes were considered as genomic CNVs.
Conversely, regions were called duplicated if 10 or more adjacent probes displayed greater than a two-fold increase in hybridization signal.
However, the criteria used to identify the CNV and DMR required the involvement of three or more adjacent probes in the genome sequence having significant differential hybridization.
DMRs were defined as regions containing three or more adjacent probes within a defined lasso region showing unidirectional changes in methylation that attained nominal significance (unadjusted p ≤ 0.05) in the DMP analysis.
To discern the relationship between Set1 binding and the transcriptional status of its targets, we ranked 290 protein-coding genes with significant Set1 binding (chromatin immunoprecipitation (ChIP) fold enrichment ≥2 at three or more adjacent probes) according to their expression levels.
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ChIP-enriched regions were defined as three or more adjacent microarray probes with fold-enrichment greater than a two-Gaussian null distribution threshold (greater than twofold enrichment).
The pnorm function used to identify differentially methylated CpG sites in the 47,XXY patient and the comb-p package was used to identify 500bp regions of 2 or more adjacent differentially-methylated probes.
For all samples, individual probes were grouped into sets of five continuous probes (unless adjacent probes were more than 5 kb apart) and their log2 value was averaged.
Finally, we compared signal intensities generated from individual gene transcripts covered by two or more adjacent but non-overlapping S. aureus probes.
Not only a larger number of individuals studied, but the correlation structure from adjacent probes on the microarray is more complex, peaks are expected to be more variable in size and shape and in certain applications more numerous (requiring different approaches for multiple comparisons) and there can be more serious measurement error problems.
The next year, 16 more adjacent acres were purchased.
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more adjacent loci
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