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The parameters and their associated codes are listed in Table 2. Observed level data were checked for quality prior to interpolation to standard levels.
The resulting sequences were checked for quality using Chromas Lite 2.1.1.0 (Technelysium Pty Ltd).
All PCR products were checked for quality against an EZ Load Precision Molecular Mass Ruler Bio-Radd Laboratories, Hercules, CA, USA) on 1% agarose gels (with a TAE buffer base) by standard gel electrophoresis, followed by ethidium bromide staining and imaging using the Fluor-S MultiImager system (Bio-Rad Laboratories).
RNA samples were checked for quality on the Agilent 2100 Bioanalyzer.
Following scanning, arrays were checked for quality using Affymetrix Genotyping Console.
RNA samples were checked for quality and quantified using the Agilent 2100 Bioanalyser (Agilent Technologies) according to the manufacturer's instructions.
To monitor quality during data collection, the principal investigator visited the teams at least monthly, and all completed forms were checked for quality and completeness.
Scanned microarray CEL output files were checked for quality assurance and raw signal intensities were RMA normalized using the affy package [61].
Prior to quantitation all DNA samples were checked for quality using 2% agarose gel electrophoresis, and obviously degraded samples were excluded from the pooling analysis.
Based on genotype data samples were checked for quality of genotyping based upon genotype call rate per sample, population outliers using Structure [32], [33] and Plink and for cryptic relatedness and gender discrepancies with Plink [30].
Resulting reads were checked for quality using FastQC [ 36].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com