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For data filtering and data analysis, spots with background-corrected signal intensity (median) in both channels that were less than two fold of background intensity (median) were rejected from further analysis.
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Background was subtracted from the median pixel intensity values for Cy3 and Cy5, and data points were removed if intensities did not exceed 2-fold of background levels for both Cy3 and Cy5.
Each wash was seen to produce a 2-fold removal of background contaminant, with the contamination in the two-wash device in all cases to be below 0.6%.
For the comparative genome analysis, low quality features and features with a signal level less than two-fold of the background plus two-fold of the background standard deviation was filtered from the initial raw data set.
Spots with background-corrected signal intensity (median) less than two-fold of the background intensity (median) in both channels were excluded from further analysis.
Adjusting flash strength (and dividing the response by the flash strength to measure gain) allowed us to probe a ∼10,000-fold range of backgrounds.
Second, the spike responses of toad ganglion cells exhibit an ∼10-fold range of backgrounds over which the threshold required to reach a criterion spike rate increases in proportion to the square root of the background (Donner et al., 1990).
"Exposition de Sèvres" (1855), Louis Robert's image of an elaborately carved stone urn, is especially marvelous: oxidation in the folds of the background curtains makes the image almost three-dimensional.
Spots with signal intensity (median) in the channel of Reference DNA less than two folds of local background intensity (median) were rejected from further analysis.
Consistent with results from an earlier U.S. Environmental Protection Agency meta-analysis of three occupational cohorts, Crump et al. [Environ Health Perspect 111 681-687 (2003)] recently concluded that "dioxin TEQ [toxic equivalent] exposures within roughly 3-fold of current background levels may be carcinogenic" to humans.
Features with signal intensities less than 2.5 fold of the mean background signal were removed, and ratios were normalized using housekeeping gene normalization [ 16] and were averaged and log transformed.
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