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Processed expression chip used in the GSE3744 dataset contained multiple probes that mapped to LRP6.
The following rules were applied for grouping the exRefSeq genes with multiple probes that represent conflicting group assignments.
However, the most pertinent methylation differences are represented by the same directional log2 (HpaIIr/McrBCr) changes across multiple probes that are in close proximity to one another on the genome; thus, we identified loci with more than two differentially methylated probes.
Multiple probes that mapped to the same or different exons of a specific gene were excluded.
We removed single probes that match more than one gene, as well as sets of multiple probes that match a single gene.
In this case, loss of some markers due to labeling variation can be disregarded since there are multiple probes that can be used to evaluate the presence or absence of the gene or locus.
Similar(46)
However, we cannot eliminate the possibility that each peak contains more than one probe, and that either hybridization occurs through partial hybrids between a single target and multiple probes, or that multiple probe-target interactions occur within each peak.
A gene was said to be detected at p < 0.05 level if the mean signal intensity from multiple probes for that gene was significantly higher (at the level of p < 0.05) than the negative control on the same chip.
A locus was said to be detected at p < 0.05 level if the mean signal intensity from multiple probes for that CpG locus was significantly higher (at the level of p < 0.05) than the negative control on the same chip.
Multiple, highly reactive probes that are specific for a particular organism can then be put on the array for further iterative evaluation.
This includes probes matching multiple genes, and probes that fail to meet the minimum criterion of 3 probes to form a probe set.
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