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After applying these data quality thresholds, data for 250 SNPs in the 42 selected genes (Supplementary Table A) were available for 377 ALL cases and 448 controls.
After applying these data quality thresholds, data for 238 SNPs in the 32 selected genes were available for 377 ALL cases and 448 controls.
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Figure 3 shows that increasing the RA data quality threshold reduces the difference between the MLST and RA trees (both 19- and 36-strain datasets) as we predicted.
In conclusion, all the data were within data Quality Control thresholds, according to Affymetrix Expression Console specifications.
In summary, all the data were within data Quality Control thresholds, according to the Affymetrix Expression Console specifications.
For example, we will add control buttons for users to customize interaction data quality filter thresholds, and to select a subset of retrieved protein interactions for downloading into spreadsheet programs.
Quick visualization of ChIP-seq results, when presented as a ChIP read distribution or protein-binding profile map, is an invaluable means for rapidly assessing data quality and setting threshold parameters for peak calling.
Developing a set of measures for assessing data quality and determining appropriate thresholds will be important for ensuring high-quality 4DN data.
After the application of stringent quality thresholds, data from 4,506 markers in 2,692 individuals were included in the analysis.
Of the 6144 SNPs, 3934 (64.0%) yielded data that met our quality thresholds according to the GoldenGate genotyping system (Uchiyama et al. 2012).
Data is said to be of research standard quality if the record satisfies pre-specified minimum data quality criteria that include thresholds for practice death recording and missing data [ 13, 14].
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