In addition to these QC steps, probes that contained <95% of signals detectable above background signal (detection P-value of <0.01; N = 7938) were excluded from analysis.
This mild threshold was used to minimize the chances of false negative associations and evaluate in subsequent steps probes with strong or moderate associations with glioblastoma per se.
In addition to these QC steps, probes that contained <95% of signals detectable above background signal (detection P-value <0.01) (N = 7938) were excluded from analysis.
As a first step, probe sets called 'Absent' over all conditions and replicates were removed (5,792).
After this second normalisation step, probe hybridisation values were all comparable, while pool hybridisation values were not significantly changed.
In summary, to obtain reasonably accurate Cynomolgus macaque methylation results from the Human Infinium 450K array, we suggest a three-step probe filter: bitscore >70, uniqueness of sequence match, and no mismatches near to the CpG site.
For this latter step probe sets were mapped to ENSEMBL genes using the mapping file (HuEx-1_0-st-v2, U-Ensembl49, G-Affy.cdf) generated by the aroma.affymetrix team [ 49].
DNA was sheared to between 1 and 2 kb by sonication for three 15-second pulses with a 1.5 mm step probe equipped sonicator set to a magnitude of 30%.
For measuring the approach to a flat surface and for the profile across a square step, probe total resistances (series + access; Rs + Ra) were 29 and 30 MΩ, respectively, whereas for the topographical imaging of erythrocytes, the probe resistance was 125 MΩ.
These approaches may not always synergistically intensify EMIs, however, step-by-step investigation probing optimal combinations should maximally enhance EMIs to achieve successful human hair follicle bioengineering.
