Hello,
I am trying to run WGCNA on my dataset for a single trait. When running the constructNetworks() function, I am met with the following error
Error in (new("standardGeneric", .Data = function (x, y = NULL, use = "everything", : unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)
I've also included a few lines of the output before the error:
....checking kME in modules.. ..removing 1131 genes from module 1 because their KME is too low. ..removing 1131 genes from module 2 because their KME is too low. ..removing 1076 genes from module 3 because their KME is too low. ..removing 699 genes from module 4 because their KME is too low. ..removing 666 genes from module 5 because their KME is too low. ..removing 305 genes from module 6 because their KME is too low.
Finally, I've attached both the expression file (this is only a subset of the expression file because the actual file itself is too big) and the phenotype file here. Please let me know if any other information is needed.
norm_counts_subset.csv
sampleTable.txt
Hello,
I am trying to run WGCNA on my dataset for a single trait. When running the constructNetworks() function, I am met with the following error
Error in (new("standardGeneric", .Data = function (x, y = NULL, use = "everything", : unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)I've also included a few lines of the output before the error:
....checking kME in modules.. ..removing 1131 genes from module 1 because their KME is too low. ..removing 1131 genes from module 2 because their KME is too low. ..removing 1076 genes from module 3 because their KME is too low. ..removing 699 genes from module 4 because their KME is too low. ..removing 666 genes from module 5 because their KME is too low. ..removing 305 genes from module 6 because their KME is too low.Finally, I've attached both the expression file (this is only a subset of the expression file because the actual file itself is too big) and the phenotype file here. Please let me know if any other information is needed.
norm_counts_subset.csv
sampleTable.txt