Tree cut height for Consensus data input not working I have tried different combination of tree cut heights but im getting the exprSize as one sample as full the other one as empty .

# Choose the "base" cut height for the female data set
baseHeight = 135
# Adjust the cut height for the male data set for the number of samples
cutHeights = c(135, 145*exprSize$nSamples[2]/exprSize$nSamples[1]);
# Re-plot the dendrograms including the cut lines
pdf(file = "SampleClustering.pdf", width = 12, height = 12);
par(mfrow=c(2,1))
par(mar = c(0, 4, 2, 0))
for (set in 1:nSets)
{
  plot(sampleTrees[[set]], main = paste("Sample clustering on all genes in", setLabels[set]),
       xlab="", sub="", cex = 0.7);
  abline(h=cutHeights[set], col = "red");
}
dev.off();


My figure 

When i see the cutHeights and exprSize i do see its higher than 120 but still i get only one set of sample which is 55 whereas the my other set which is 

exprSize
$nSets
[1] 2

$nGenes
[1] 8213

$nSamples
[1] 55 47

$structureOK
[1] TRUE


This is after tree cut 

exprSize
$nSets
[1] 2

$nGenes
[1] 8213

$nSamples
[1] 55  0

$structureOK
[1] TRUE

&gt; cutHeights
[1] 135.0000 123.9091


Im not able to figure out what is wrong
Your data don't have obvious outliers so you don't have to worry about removing them. The problem is that both sets show prominent sample clusters. I would try to figure out what drives those clusters (is it technical or biological), and whether the variation should be removed. See the comments in WGCNA FAQ under point 5 (My data are heterogeneous. Can I still use WGCNA?). This looks like data from GEO, so look into the sample annotation for these data sets and see if any of the recorded sample characteristics align with the clusters you see in the sample trees.