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In this manner, a background level was calculated as an average weekly incidence over a six-week period before the first virus isolation and a six-week period after the last isolation.
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The background level is calculated as an aggregate summary of six to eight control probes with no target transcript.
The median and standard deviation of background levels were calculated.
Background levels were calculated locally for each spot using the median of the background pixels.
Background levels were calculated for each image stack as the average mean intensity value of several larger distributed areas devoid of any cellular processes (i.e., signal).
When we considered a transcription factor to be active at a significance level of 5% (the z-score corresponding to each activity level was calculated from the background distribution estimated from all activity levels), on average 13 TFs were active per condition in our data set (11 – in the Affymetrix data set).
Average methylation level was calculated using the methylKit software package.
The DNA methylation level was calculated as 5mdC/ dC + 5mdC) × 100%.
Expression level was calculated using the ddCT method.
Each sample was measured relative to the background, and expression levels were calculated as the Optical Density (OD) ratio between the β-actin and L1-CAM of each sample.
Each sample was measured relative to the background and phosphorylation levels were calculated as the ratio between the results from the antibody directed against the phospho-proteins divided by the antibody directed against the phosphorylation state-independent form of the proteins.
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