Several tools have already been developed for merging paired-end reads, such as the merge module in CLC, PEAR, FLASH, PANDAseq, Stitch and FastqJoin [ 22– 27].
GFP-labeled SPB and tdTomato-labeled cell membrane fluorescence were excited with the 488 nm and 561 nm lines, respectively, from a LMM-5 solid state laser merge module controlled with an ATOF (Spectral Applied Research Inc., Canada).
By the same token, the plastic moments of resistance of the merging modules or the reassembled structure may be expressed as: M i P = M ¯ i P + M ¯ i + 1 P and N i P = N ¯ i P = M ¯ i P (2).
The minimum module size was set to 30 and the cut-off for merging modules was set to 0.25.
The minimum module size was set to 40 genes and the height for merging modules was set to 0.25, which required at least 25% dissimilarity among modules in expression.
Sixth, due to missing HADS measurements after each module, we were not able to perform a repeated measurement ANOVA and merged modules with similar content to blocks (cognitive vs. exposure block).
After setting a minimum module size of 30 and merging modules with highly correlated (r > 0.85) eigengenes (defined as the first principal component of a given module and may be considered as a representative of the gene expression profiles in that module), a total of 30 modules were found (excluding the grey module, which is used to hold all genes that do not clearly belong to any other module).
The merging module removes the smaller ones by combining smaller empty space into a large one, thus facilitating the placement of the larger rectangles at the lower Y-coordinate.
That is, this mechanism also corresponds to the merging module mechanism [ 34], which induces hierarchical modularity.
Weighted adjacency matrices were computed, modules were defined using the cut Tree Dynamic function (which selects good dendrogram cutoffs) and similar modules were merged using merge Close Modules (which compensates for the high sensitivity of WGCNA).
Such effects entail the failure of modularity optimisation to detect modules smaller than a scale which depends on the size of the network and the degree of inter-connectedness of the modules, as the algorithm tends to merge small modules to achieve larger modularity values [ 33, 37, 38].
