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I am not sure if that is normal to get some (or one) modules that only contain 1 gene when running WGCNA. I believe I have set the minModuleSize = 20
. If that is not uncommon, how should we explain the presence of a module with only 1 member? Is it possible that all other "members" were excluded during the module trimming? I am running a signed network using power = 8
, deepSplit = 2
, and pamState = FALSE
, I ran the blockwiseModules()
with the following options that I was copied from the user manual:
net = blockwiseModules(
# Input data
datExpr,
weights = NULL,
# Data checking options
checkMissingData = TRUE,
# Options for splitting data into blocks
blocks = NULL,
maxBlockSize = 50000,
blockSizePenaltyPower = 5,
# nPreclusteringCenters = as.integer(min(ncol(datExpr)/20,
# 100*ncol(datExpr)/maxBlockSize)),
randomSeed = 54321,
# load TOM from previously saved file?
loadTOM = FALSE,
# Network construction arguments: correlation options
corType = "bicor",
maxPOutliers = 1,
quickCor = 0,
pearsonFallback = "all",
cosineCorrelation = FALSE,
# Adjacency function options
power = power_option,
networkType = signness,
replaceMissingAdjacencies = FALSE,
# Topological overlap options
TOMType = signness,
TOMDenom = "min",
suppressTOMForZeroAdjacencies = FALSE,
suppressNegativeTOM = FALSE,
# Saving or returning TOM
getTOMs = NULL,
saveTOMs = TRUE,
saveTOMFileBase = paste0(data_source, "_", test_net, "_blockwiseTOM_D", tree_deep, "_", signness, "_P", power_option, "_pam", pam_option),
# Basic tree cut options
deepSplit = tree_deep,
detectCutHeight = 0.995,
minModuleSize = 20,
# Advanced tree cut options
maxCoreScatter = NULL, minGap = NULL,
maxAbsCoreScatter = NULL, minAbsGap = NULL,
minSplitHeight = NULL, minAbsSplitHeight = NULL,
useBranchEigennodeDissim = FALSE,
# minBranchEigennodeDissim = mergeCutHeight,
stabilityLabels = NULL,
stabilityCriterion = "Individual fraction",
minStabilityDissim = NULL,
pamStage = pam_option, pamRespectsDendro = TRUE,
# Gene reassignment, module trimming, and module "significance" criteria
reassignThreshold = 1e-6,
minCoreKME = 0.5,
# minCoreKMESize = minModuleSize/3,
minKMEtoStay = 0.2,
# Module merging options
mergeCutHeight = 0.15,
impute = TRUE,
trapErrors = FALSE,
# Output options
numericLabels = TRUE,
# Options controlling behaviour
nThreads = 0,
useInternalMatrixAlgebra = FALSE,
useCorOptionsThroughout = TRUE,
verbose = 2, indent = 1)