The traditional approach segments noisy probe-level data in individual tumors (dividing the genome into regions of equal copy number) [11], [12], detects aberrations with a global threshold, and heuristically defines boundaries of regions of frequent change [13], [14].
These data were used to show a similar trend to that observed in the original paper, that noisy probes show greater within tissue methylation variance than non-noisy probes.
We used these data to show that noisy probes can affect the overall ability to detect meaningful biology.
First, the recommended noisy probes (in total 190672 (75,292 Infinium I and 115,380 Infinium II)) were removed from the analysis pipeline.
Initially, the potential noisy probes (319,545 or 65% of the probes, Table 1) were removed and then differentially methylated probes were determined and mapped to refGenes.
Thus, Figure 6 supports the use of subinterval averaging of the CPM as an effective means of averaging across noisy probes for these data.
A comparison of the SD distributions for the 4 blood samples shows that the high-quality KEEP set of probes shows significantly lower standard deviations in beta-value than the DISCARD set of noisy probes (p-value = 1.97e-84) based on Wilcox-test [ 39].
This choice was liberal enough to include most probe sets and to exclude the noisiest probe sets with the weakest signal.
By using a direct comparison with whole-genome bisulfite sequencing data, only the probes showing a noisy signal were removed thereby maximizing the number of probes retained for subsequent analysis.
The opposition, meanwhile, has stepped up its noisy demands for a parliamentary probe into the affair.But Mr Raja's exit, following as it does two high-profile political firings in as many weeks, suggests the government has a new appetite for tackling graft.
Since probe intensities are noisy, both SNP and fine-tiling arrays require many probes to span the deletion for accurate measurement.
