WGCNA: minModuleSize is not responding correctly
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Entering edit mode
10 weeks ago

This is a cross question posted in bioconductor.

I am running the WGCNA, but getting an error. As I can see that the minimum module size that I am getting is 1, but by default it should not give anything less than 30.

modules <- blockwiseModules(transcriptomics,
                                    power = 9, 
                                    networkType = "signed", 
                                    TOMType = "signed",
                                    corType = "bicor",
                                    numericLabels = TRUE,
                                    saveTOMs = save_TOM,
                                    saveTOMFileBase = "TOM",
                                    verbose = 3,
                                    maxBlockSize=8000, 
                                    nThreads = 11)


rownames(modules$MEs) <- rownames(metatranscriptomics)
names(modules$colors) <- colnames(metatranscriptomics)
hubs_M <- chooseTopHubInEachModule(metatranscriptomics, modules$colors, power = 9, omitColors = "0")

Error in hubs[m] <- colnames(adj)[hub] : replacement has length zero

I checked, how many modules I got-

table(modules$colors)

    0     1     2     3     4     5     6     7     8     9    10    11 
60409  8629  3608  3204  1909   483   111    88    32    31     4     1
table(names(modules$colors) == colnames(metatranscriptomics))

 TRUE 
78509

I have looked at this post- https://bioinformatics.stackexchange.com/questions/17598/wgcna-hub-genes-error

But I can't solve this issue. Any suggestions?

RNA-Seq WGCNA • 294 views
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Entering edit mode

You can use intramodularConnectivity to calculate the connectivity of genes and identity the top hub in each module (gene with the highest connectiviy).

Regarding the error

Error in hubs[m] <- colnames(adj)[hub] : replacement has length zero

Can you try to convert the module names with colors?

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