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To check for systematic biases in fluorescent dye incorporation, we performed a series of self-self hybridisations, i.e., an identical sample was labelled with both the Cy3 and Cy5 fluorochrome and hybridised on the same array.
Permutation tests were used to check for systematic up-regulation or down-regulation of the genes bound by E2f4 in all tissues (as identified from the Microarray Analysis explained below).
To check for systematic differences between tests one and two (systematic bias), McNemar analyses were applied with a p value of 0.05 as significant.
Quantile-quantile plots were used to check for systematic genotyping error or bias due to unaccounted underlying population substructure.
The overall the stable isotope peak intensities were then compared to check for systematic errors in labeling and protein concentration.
Student's t test for paired observations was used to check for systematic errors in anthropometric measurements.
To check for systematic error between the two measurements, the Wilcoxon's signed rank test was used.
To check for systematic differences, excluded cases missing one or two items (n = 627) were compared with cases included in the analyses.
We did not include blinded duplicates in the genotyping dataset, and therefore we did not have the opportunity to check for systematic genotyping errors.
One possibility to check for systematic errors in phylogenetic analyses is the comparison of the results based on independent data sets.
For each predicted peak, the difference between the predicted and actual start and end of the genome location were calculated to check for systematic over- or under-estimation of peak width.
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