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Finally, the similarity between samples was estimated by calculating the chosen distance (e.g., -norm or -norm) between feature histograms.
The significance of factorial effects and differences between samples was estimated by means of ANOVA/MANOVA and post hoc Student's t- and LSD-tests in STATISTICA data analysis software system (StatSoft, Inc., Tulsa, OK, USA).
The error between samples was estimated using the standard deviation of the mean from three replicates measured per treatment.
Euclidean distance between samples was estimated based upon FPKM for the 15,616 protein-coding mRNAs detected in at least 25%% of samples (i.e., at least 7 of 28 samples).
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In practice, distances between samples are estimated using the same σ value for all cases and must be carefully selected.
Quantitative expression differences between samples were estimated using cDNA from male and female vegetative, immature and mature reproductive stages, obtained using the Invitrogen Superscript™III First strand cDNA synthesis kit according to manufacturer's instructions.
Significance of the difference between means in two samples was estimated by the t-test p-value.
The heterogeneity between the three Scandinavian samples was estimated by calculating the fixation index of the all SNPs in the healthy controls, using Stucture2.2 [34].
Allelic imbalance of RNA between tumor and normal samples was estimated by calculating a ddCT value for each genomic coordinate assayed, by simply subtracting the dCT value of the normal cDNA sample from the corresponding dCT of the tumor cDNA sample.
For each gene, the log2 fold change between parous and nulliparous samples was estimated as the difference in median Ct values.
Genetic differentiation between all pairs of geographical samples was estimated at each sampling site.
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