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This type of plot reflects the similarities and differences between all samples in relation to the 782 significant genes.
HCA is an unsupervised clustering technique that examines the interpoint distances between all samples in row space and represents them in a dendrogram.
This approach is thus robust as long as not more than 70% of all genes on the array are differentially expressed between all samples in the batch, which is rarely the case.
In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets.
CVA (canonical variates analysis) was used to calculate the Procrustes distances between all samples in a given data subset (Procrustes distances are a part of the CVA output in MorphoJ).
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A comparison is also done between single scan configuration including all samples in a single A4 (HP) or A3 (EPSON) format area and multiple scan procedure where each sample is scanned separately on its own.
The distribution of carcinogenic PAHs also showed no significant difference between groups (P = 0.85 for all samples in each group, Table 4).
Spearman correlation between all samples was computed in order to examine the variance and the relationship of global gene expression across the samples, using genes with raw counts larger than zero.
An extreme example of the latter was provided by the single fungal lineage shared between all sampled colonies in western Africa of the three divergent genera Microtermes, Ancistrotermes and Synacanthotermes [ 9].
PCoA analysis of Unifrac distances calculated between all samples showing the differences in representation of taxa between the samples.
There were no differences in rancidity between all samples at day 0 of storage (p > 0.05).
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