From the middle of the 18th fairway he hit the flagstick with his approach and saw his ball bounce off the green - an injustice he quickly corrected by chipping in for an outrageous birdie, to finish alongside Woods and Geoff Ogilvy, who played the back nine in 31 shots, five under.
This leads to a more accurate correction compared with calculating GC-content bias (λ and λ gc) for the control data only and then correcting the ChIP and control densities based on the same λ values.
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Extracted data were transferred into Microsoft Excel (Microsoft Corporation, Reading, UK) where all data were transformed to Log base 2. Transformed data were then corrected within each chip using the median percentile shift to 5 abundantly expressed positive control probes on each array.
We quantified the precipitated fractions by using real-time PCR amplification (Fig 2B) and corrected (in all ChIP experiments of this study) the obtained values against background precipitation with a non-immune IgG control antiserum.
For Illumina, microarray results were normalized by quantile normalization and LIMMA was used to calculate significant differences between groups using slide number as a covariate to correct for chip-specific effects.
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Here the "height" and "width" parameters, αc and βc, characterize the vertical and horizontal dimensions of the corrected hook curve of chip "c" (see Figure 7 and Figure 8) which in turn are related to the mean binding characteristics averaged over all probes of the chip, i.e., log K c P, h ≈ 〈 log K p P, h 〉 chip (P = PM, MM, h = N, S).
Probe-set summary and background correction of expression values were performed by using the RMA algorithm (ArrayAssist ExonRMA), and chip-to-chip variation was corrected by using quantile normalization.
