WGCNA error during network construction

Question

[akansha.gitanjali]

I am performing WGCNA analysis on my RNAseq dataset and getting this error message:

    >net = blockwiseModules(expression, power = 6,
        +                        TOMType = "unsigned", minModuleSize = 30,
        +                        reassignThreshold = 0, mergeCutHeight = 0.25,
        +                        numericLabels = TRUE, pamRespectsDendro = FALSE,
        +                        saveTOMs = TRUE,
        +                        saveTOMFileBase = "SW_TOM", 
        +                        verbose = 3)
         Calculating module eigengenes block-wise from all genes
           Flagging genes and samples with too many missing values...
            ..step 1
          ..Excluding 722 genes from the calculation due to too many missing samples or zero variance.
            ..step 2
         ....pre-clustering genes to determine blocks..
           Projective K-means:
           ..k-means clustering..
           ..merging smaller clusters...
        Block sizes:
        gBlocks
           1    2    3    4    5 
        4999 4998 4945 4424 4306 
         ..Working on block 1 .
        Error in blockwiseModules(expression, power = 6, TOMType = "unsigned",  : 
          REAL() can only be applied to a 'numeric', not a 'integer'

How do I solve this error? The code I used is given below.

library(WGCNA)
#Setting string not as factor
options(stringsAsFactors = FALSE)
#Enable multithread
enableWGCNAThreads()
#Reading the raw data (rows are the sample and columns the genes)
SWexpressiondata = read.csv("edgeR_normalized.csv")

#Create a new format expression data - remove gene name column
expression = as.data.frame(expressiondata[, -c(1)]) 
expression = t(expression)

#Column 1 -  gene names
colnames(expression) = expressiondata$genes
rownames(expression) = names(expressiondata)[-c(1)]

#Group data in a dendogram to check outliers
sampleTree = hclust(dist(expression), method = "average")
dev.off()
sizeGrWindow(12,9)
par(cex = 0.6)
par(mar = c(0,4,2,0))
plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5, 
     cex.axis = 1.5, cex.main = 2)


# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to = 20, by = 2))
# Call the network topology analysis function
sft = pickSoftThreshold(expression,             # <= Input data
  #blockSize = 30,
  powerVector = powers,
  verbose = 5)
# Plot the results:
sizeGrWindow(9, 5)
par(mfrow = c(1,2));
cex1 = 0.9;

# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[, 1],
     -sign(sft$fitIndices[, 3]) * sft$fitIndices[, 2],
     xlab = "Soft Threshold (power)",
     ylab = "Scale Free Topology Model Fit, signed R^2",type="n",
     main = paste("Scale independence"))

text(sft$fitIndices[, 1],
     -sign(sft$fitIndices[, 3]) * sft$fitIndices[, 2],
     labels = powers, cex = cex1, col = "red")

# this line corresponds to using an R^2 cut-off of h
abline(h = 0.90, col = "red")
# Mean connectivity as a function of the soft-thresholding power
plot(sft$fitIndices[, 1],
     sft$fitIndices[, 5],
     xlab = "Soft Threshold (power)",
     ylab = "Mean Connectivity",
     type = "n",
     main = paste("Mean connectivity"))
text(sft$fitIndices[, 1],
     sft$fitIndices[, 5],
     labels = powers,
     cex = cex1, col = "red")

[andres.firrincieli]

possible solution: link

[akansha.gitanjali]

Using the above solution I get another error: "non-numeric argument to mathematical function"

> bwnet = blockwiseModules(expression, maxBlockSize = 5000,
+                         power = 10, TOMType = "unsigned", minModuleSize = 100,
+                         reassignThreshold = 0, mergeCutHeight = 0.25,
+                         numericLabels = TRUE,
+                         saveTOMs = TRUE,
+                         saveTOMFileBase = "SpodopteraTOM-blockwise",
+                         verbose = 3)
 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
Error in abs(datExpr) : non-numeric argument to mathematical function

[andres.firrincieli]

check the expression matrix (expression) because you clearly have non-numeric values.

Also, the expression matrix is uploaded as SWexpressiondata = read.csv("edgeR_normalized.csv") but along the code you use a different matrix expression = as.data.frame(expressiondata[, -c(1)])

[akansha.gitanjali]

I guess I was making some mistake. This code worked for me:

expression[1:20, 1:19323] <- as.numeric(as.character(expression[1:20, 1:19323]))