blockwiseModule crashes in the end and doesn't generate modules
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@17087816
Last seen 13 months ago
United States

Hi,

I am trying to generate my modules using blockwiseModules, with the following code:


net <- blockwiseModules(data_TRAP, power = 8,
                       TOMType = "unsigned", minModuleSize = 30,
                       reassignThreshold = 0, mergeCutHeight = 0.25,
                       numericLabels = TRUE, pamRespectsDendro = FALSE,
                       saveTOMs = TRUE,
                       saveTOMFileBase = "GADD34_BDNF_TOM",
                       maxBlockSize = 15000,
                       deepSplit = 2.5,
                       verbose = 3)


sessionInfo( )

The process runs smoothly, until it gets to the end, when this warning comes up:


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 GADD34_BDNF_TOM-block.1.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 1 genes from module 1 because their KME is too low.
     ..removing 2 genes from module 40 because their KME is too low.
     ..removing 1 genes from module 56 because their KME is too low.
Error in (new("standardGeneric", .Data = function (x, y = NULL, use = "everything",  : 
  unused arguments (weights.x = NULL, weights.y = NULL, cosine = FALSE)

My object is then not generated, and TOM block is not saved. Would anyone know the problem? Thanks.

WGCNA • 1.7k views
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Re: drift boss

Have you fixed this problem yet?

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Re: basketball

I think this proplem has been solved, it seems.

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ATpoint ★ 4.2k
@atpoint-13662
Last seen 47 minutes ago
Germany

WGCNA is not a Bioconductor package, you're not at the right spot here. However, googling the last line of your error (always recommended to do that) points to various reports including https://www.biostars.org/p/305714/ suggesting namespace issues.

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To resolve this issue, you should remove the weights.x, weights.y, and cosine arguments from your blockwiseModules function call. wordle

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