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The present call is based on the signal value for each gene (probe) relative to the local median background level surrounding each spot.
We removed data from spots with intensity levels lower than the median background level of 175 and log transformed and normalized data across arrays using the Lowess method.
The median background level of dioxins in soil in the lower peninsula of Michigan is 4.6 ppt, and the 97.5th percentile is 34 ppt.
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We subtracted the median background levels from unstimulated control cell cultures from the median rubella-induced responses to calculate corrected secretion values.
Vingarzan (2004) surveyed recent literature on background ozone concentrations and concluded that based on data from 1983 to 2001, median background levels in the United States ranged between 13 and 47 ppb.
The background levels achieved with restrictions were below median background levels in the general population [30 μg/L for MEP and 9.2 μg/L for MnBP for adult males sampled in 2011 2012 (CDC 2015)] and more than two orders of magnitude below peak levels observed in the subsequent exposure experiments.
Genes whose intensities were less than the median plus two standard deviations of background level were identified as null.
Genes whose intensities were less than the median plus two standard deviations of the background level were identified as null.
Log-ratios of local median background-subtracted intensity levels were analyzed.
Pregnancies fathered by workers before exposure were also assumed to have exposure at the background level and so were assigned the median referent value of 6 pg/g.
The resulting expression levels for each of the miRNAs measured by the microarrays were calculated and filtered for miRNAs expressed above a background level (background was set at 30, approximating the median signal per array).
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