Selected EDCs were derived from the results of stepwise analyses in explaining prospective total expenditures, using a full set of EDCs and a multivariate linear regression model; 19 EDCs were thus chosen (Additional file 1).
ISR was assessed using a total of 201 sample sets, selected from 31 subjects who completed all four periods of the study.
Specifically, sample labels were permuted (same permutation over all CpGs) and supervised analyses carried out on the resampled data set, using a total of 100 permutations to obtain reasonable estimates of the FDR.
Moreover two biological replicates were used in each case, producing a total set of 48 microarrays.
In this study we used a total of four different primer sets, one to quantitate copy number (H12360 and L12464), a set for the actual experiment (H6363 and L6851) and two different sets for the control experiments (H5912 and L6300, and H14838 and L15437).
The default setting was to use a total of six clusters, three for fibroglandular tissue and three for fatty tissues.
For the co-expression analysis, we calculated the mean value of each gene for a given species using the total set of the arrays used to assay that species.
Enrichment was determined using the total set of all detected proteins as the background set, and using the following settings: Similarity Term Overlap: 4; Similarity Threshold: 0.35; Initial Group Membership: 4; Final Group Membership: 4; Multiple Linkage Threshold: 0.50.
Thus, using the total set under this proportionality assumption, the percentage of chimeric TE insertions detected relative to expectation is little changed (65 out of 341, 19%).
We thus made the analysis using the total set of genes expressed in each male or female cone of the gymnosperms, independently of its expression in the other, female or male, cone.
