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Probes with "absent" signals in all samples (lower than or near to background levels) were removed from further analysis.
As before, probe sets expressed below background levels were removed, first by discarding all exons from genes that were previously removed at the gene level due to lack of detectable expression, followed by repeating the filtering procedure on the remaining exons.
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Genes below this level were removed.
Probe sets with background level signal intensities were removed by filtering out probe sets where the lower quantile was below five.
To properly correlate the intensity in the atomic columns with their composition, the background level has been removed from the experimental HAADF-STEM images.
At this point, most background regions were removed.
Background peaks were removed that occurred in the controls.
The background was subtracted and data points with a value below 0 after background subtraction were removed.
Background values were removed and to ensure linearity, assays were used at below 50% saturation.
Subsequently, probes with spot diameter <40 µm or intensity below background were removed.
Any spots with an intensity of less than 100 (the background level on the arrays) were removed from the analysis.
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