We also reported that this analysis was confounded by large scale differences between the study sites.
Comparisons of gene expression within the groups of vaccinated and naïve fish found large scale differences between HR and LR.
Circular genome comparisons generated with BRIG [ 49] that show large scale differences between the P. aeruginosa genomes are included as Additional file 3: Data File 5, using PAO1 as the reference, and Additional file 4: Data File 6, using a PAHM4 pseudochromosome as the reference.
Given the high habitat heterogeneity and environmental variability in these canyons and channels, we hypothesise that the nematode assemblages will be largely controlled by small-scale, local environmental conditions rather than large-scale differences between canyons or water depths.
Non-metric multidimensional scaling analysis reveals large-scale differences between the sister taxa S. frontalis and S. attenuata and the rest of the Delphininae.
Our hope in including this spatial term is to adjust for large-scale differences between AOD and PM2.5, allowing us to exploit common patterns of AOD and PM2.5 at smaller spatial scales, to the extent that they exist.
Having demonstrated large-scale differences between the rat and mouse transcriptional responses to TCDD and having shown that these differences lead to alterations in specific pathways, we next considered mechanism.
We corrected for differences in normal tissue contamination then calculated a Z score for the presence of large-scale differences between samples, as described in the Supplementary Methods file and Supplementary Figure 4. Seven pairs of tumours stood out as being significantly different (H08, H09, H10, H13, H14, H15 and H19; Supplementary Table 6).
Gene-centric analyses, as discussed above, allow construction of functional scaffolds to model metabolic interactions within a community (e.g. Warnecke et al., 2007) as well as the determination of large-scale differences between the gene complements of distinct ecosystems (e.g. Tringe et al., 2005; DeLong et al., 2006; Dinsdale et al., 2008a).
Hierarchical clustering and multidimensional scaling failed to uncover a large-scale difference between them.
