Hello,

I am doing co-expression network with WGCNA on RNA-seq data (70-200 samples). While using blockwiseModules() function, I obtain modules smaller than the module size cut-off. Namely, minModuleSize <= 20, I got modules with just 1, 2, 4, genes. It seems a kind of exception in the function.

Anybody knows how can this be possible?

Further, I can say that this happens more frequently when the soft-thresholding power < 4 (unsigned, signed hybrid networks) or power < 9 (signed networks) even if the soft-threshold criterion is satisfied. The occurrence for larger powers is negligible, still some exceptions remain.

Here the code, the most is default:

net = blockwiseModules(input_train, power = beta_value, networkType = NT, randomSeed = seed, minModuleSize = 20, corType = "bicor", mergeCutHeight = 0.15, pamStage = TRUE, pamRespectsDendro = FALSE, TOMType = "signed", saveTOMs = FALSE, maxBlockSize = 5000, numericLabels = TRUE, nThreads = 4, verbose = 3)