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However the number of undetected genes nearly trebled with a further reduction of input RNA to 5 ng using the same amplification strategy, increasing the number of genes below the background threshold to 1606.
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Any target exhibiting a mean signal below this background threshold in both glioblastoma and control samples was considered to be undetected.
The number of probesets was reduced to 14'509 by removing probesets expressed below the defined background threshold.
Previous microarray studies typically filtered out all genes with expression below the background hybridization threshold, effectively removing loci with low or no expression.
In contrast with most other microarray methods in which an "absent" measure is the result of intensities falling below a background threshold, in the context of the Illumina BeadChip platform "no call" indicates that the intensities fell outside the bounds of the clustering regions defined for AA, AB and BB genotypes, even if those intensities were high.
Any gene consistently below a background threshold level of D = .98 for all samples was eliminated from further analysis.
Any gene consistently below a background threshold level of D =.98 for all samples was eliminated from further analysis.
where Th is the background subtraction threshold normally used.
Identify the background by thresholding; 5.
Although this value was still below the tentative threshold for background (20%), the increase from 0%to18%8%, which was the largest increase among the eight localities (see Supplementary Tables 2 and 4 in the original paper [ 1]), may be important.
Data below background noise (threshold log2<4.0) were excluded from analyses (IPA version 8.5, Redwood City, CA, USA).
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