I know WCGNA is not in Bioconductor, but it seems the best place to ask, and I have a couple of doubts about how to use it.
If I understood correctly WCGNA creates an unsupervised clustering but one can create those clusters manually. With
blocks option allows to set genes to a cluster, but seems to force to put all genes to their cluster, not allowing a semi-supervised clustering. Could we impose/force to have a cluster with certain genes and "freely" cluster others?
Can other information than the expression, like GO, pathways, be used to build the clusters? AFAIK one can use a parameter, like time, treatment or alike to build the clusters, but it would be hard to create one for each GO, or pathway manually, at the gene level.
Many work related with WCGNA is done with co-expression, those genes with high expression are clustered togheter, however the correlation could be the oposite, whenever gene X is highly expressed gene Y is lowly expressed and whenever Y is highly expressed X is not much expressed.
I couldn't find any information about these questions, but I might miss them while reading the available information and tutorials. Many thanks