I believe the unclustered genes are reserved for module 0 but I can't find this anywhere online? I think I remember hearing it in one of Dr. Hovarth's lectures on YouTube. Can someone confirm this and possibly give a reference?
Yes, 0 or "grey" are reserved to genes which aren't part of a co-expressed module. See ?moduleNumber (which I think it is internally used by other functions):
"All contiguous branches below the height cutHeight that contain at least minSize objects are
assigned unique positive numerical labels; all unassigned objects are assigned label 0."
Later on, if converting it to colors with labels2numbers it is usually converted to grey.
Also see cutreeStaticColor:
"A character vector giving color labels of objects, with "grey" meaning unassigned."
Or consensusOrderMEs:
"Normally the color grey is reserved for unassigned genes; hence the grey module
is not a proper module and it is conventional to put it last."
Or blockwiseConsensusModules:
"The color "grey" and the numeric 0 are reserved for unassigned genes."
Basically you can search for unassigned in the WGCNA manual and you'll find the references.
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version 2.3.6
Perfect, thanks again Lluis! I knew it was somewhere but I couldn't figure out which part of the docs to find it. Do you have any insight on C: WGCNA | pickSoftThreshold.fromSimilarity not working for input similarity matrix using a precomputed similarity measure as input? Peter gave some insight on the error and I'm wondering if there's something I could do within R or if I need to step back to my similarity matrix creation.