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The raw intensities were background adjusted by the Subtract method.
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Next, the data were background adjusted by subtracting the median intensity value of the negative control probes.
The read count at a given position is then adjusted by the ratio of the foreground and background heptamer probabilities.
The average signal for the normalization features was calculated for each array while a scale factor (SF) for each array was calculated as follows: SF = Average NF median signal Brightest array / Average NF median signal array A scaled F532 median signal for each probe was calculated by multiplying the background adjusted median F532 signal for each feature by the scale factor for each array.
Background adjusted signals (BGSubSignal) were calculated by the Agilent Feature Extraction Software (v9.5) and filtered on the flag IsWellAboveBG.
The values are background adjusted, normalized, and log transformed.
The arbitrary values of the implants were adjusted by discounting the background [31].
Raw intensities were adjusted by subtracting the background intensity from each probe, and the data were then summarised by taking the median intensity across the 16 replicates of each probe.
Ionization rate in counts per minute (cpm) of culture supernatants was adjusted by subtracting the background cpm.
The supply conditions can be adjusted by adjusting the proportions of each.
The intensity of each sample and standard was adjusted by subtracting background intensity from the measured intensity.
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