Question: Error in (function...) thrown by WGCNA
0
gravatar for wonderfulzhu1985
2.0 years ago by
wonderfulzhu198560 wrote:

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)

wgcna R gene • 1.0k views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by wonderfulzhu198560

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.

ADD REPLYlink written 2.0 years ago by wonderfulzhu198560

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.

ADD REPLYlink written 2.0 years ago by Kevin Blighe60k
2
gravatar for wonderfulzhu1985
2.0 years ago by
wonderfulzhu198560 wrote:

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.

ADD COMMENTlink written 2.0 years ago by wonderfulzhu198560
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