Error in (function...) thrown by WGCNA

Question

[wonderfulzhu1985]

I am a newer in learning the WGCNA, and I encounter a problem detailed below.

I have do many tries to tackle the problem by adjust the parameters. I also try many methods as the other author do in some literature. while they cannot get rid of the warning and acquire the module.

I deeply appreciate the help from you to tackle it.

WGCNA::blockwiseModules(datExpr,
                        power = 4,
                        TOMType = "unsigned",
                        minModuleSize = 30,
                        reassignThreshold = 0,
                        mergeCutHeight = 0.25,
                        numericLabels = TRUE,
                        pamRespectsDendro = FALSE,
                        saveTOMs = TRUE,
                        saveTOMFileBase = "femaleMouseTOM",
                        verbose = 3)


Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
..Working on block 1 .
TOM calculation: adjacency..
..will not use multithreading.

Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file femaleMouseTOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..removing 336 genes from module 1 because their KME is too low.
..removing 261 genes from module 2 because their KME is too low.
..removing 61 genes from module 3 because their KME is too low.
..removing 31 genes from module 4 because their KME is too low.
..removing 22 genes from module 5 because their KME is too low.
..removing 3 genes from module 6 because their KME is too low.
..removing 5 genes from module 7 because their KME is too low.

Error in (function (x, y = NULL, use = "everything", method = c("pearson", : unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)

Another possibly related post: Error in (function...) thrown by WGCNA tutorial (R)

[wonderfulzhu1985]

I also do the methods provided by three friendly experts in the block of Kristin Muench who also encounter the same problem. However I also can not tackle the problem.

[Kevin Blighe]

Can you state specifically what you tried? The solution that worked for Kristin was to restart the computer, reload R, re-install WGCNA (my recommendation is to do it via biocLite()), and then proceed from there.

Also update your version of R.

I think that it's namespace issue between the base R function cor() and WGCNA's own version of cor(), which have both diversified from each other, like gene paralogues.

Answer 1

[wonderfulzhu1985]

I think I tackle the problem. There is a conflict between the WGCNA and the other packages. the other package have a function the same as the other in WGCNA in the run r studio. when I library no packages other than WGCNA, the program runs well and get the module.