Hello,

I have a question regarding the TOMType parameter in WGCNA blockWiseModule function.

I am interested in distinguishing positively and negatively correlated groups of genes, therefore I set networkType = "signed". By mistake, though, I put TOMType = "unsigned". Specifically:

net = blockwiseModules(data ,power= 6, TOMType ="unsigned", corType="pearson", networkType = "signed", minModuleSize = 30, reassignThreshold = 0, mergeCutHeight = 0.25, numericLabels = TRUE, pamRespectsDendro = FALSE,saveTOMs = T, verbose = 3)

I looked at the documentation but it still isn't clear to me what choosing TOMType = "unsigned" implies.
Additionally, I ran the function again changing to TOMType="signed" and the resulting modules seem to be very similar (almost all the same genes).

Is choosing NetworkType="signed" enough to retain the sign in the resulting modules?

Many thanks in advance for your help.

Aurora

TOMType options handles how should conflicting TOMs be handled (TOM between gene A and B is +, between A and C is +, and between B and C is -), usually there are few conflicts that's why it doesn't make much of a difference.

The NetworkType option is described in the adjacency function. There it says:

for type = "unsigned", adjacency = |cor|^power; for type = "signed", adjacency = (0.5 * (1+cor) )^power; for type = "signed hybrid", adjacency = cor^power if cor>0 and 0 otherwise

So if you want to keep the genes positevely correlated in the same module you should use the "signed hybrid" option.

Thank you very much Lluìs, sorry I hadn't seen your reply.

Would you suggest using "signed hybrid" in general? Is there any advantage except being sure to keep only positive correlations?
If I look at genes belonging to my modules they seem to be positively correlated, but indeed from the specifications it could be that I included some negatively correlated ones.

Thank you again!

Aurora