WGCNA error
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0
Entering edit mode
@169594ea
Last seen 5 months ago
United Kingdom

Hi everyone,

I need help please. I keep getting this error in the WGCNA What could I be doing wrong?

Thanks in advance

[1] 20  3
> dim(moduleTraitCor)
[1] 401   3
> class(design2)
[1] "matrix" "array" 
> class(moduleTraitCor)
[1] "matrix" "array" 
> # Display the correlation values within a heatmap plot
> labeledHeatmap(Matrix = moduleTraitCor,
+                xLabels = names(design2),
+                yLabels = names(MEs),
+                ySymbols = names(MEs),
+                colorLabels = FALSE,
+                colors = greenWhiteRed(50),
+                textMatrix = textMatrix,
+                setStdMargins = FALSE,
+                cex.text = 0.5,
+                zlim = c(-1,1),
+                main = paste("Module-trait relationships"))
Error in labeledHeatmap(Matrix = moduleTraitCor, xLabels = names(design2),  : 
  Length of 'xLabels' must equal the number of columns in 'Matrix.'




sessionInfo( )
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] flashClust_1.01-2           WGCNA_1.70-3                fastcluster_1.2.3           dynamicTreeCut_1.63-1      
 [5] edgeR_3.32.1                limma_3.46.0                DESeq2_1.30.1               SummarizedExperiment_1.20.0
 [9] Biobase_2.50.0              MatrixGenerics_1.2.1        matrixStats_0.61.0          GenomicRanges_1.42.0       
[13] GenomeInfoDb_1.26.7         IRanges_2.24.1              S4Vectors_0.28.1            BiocGenerics_0.36.1        

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2       ellipsis_0.3.2         class_7.3-19           htmlTable_2.3.0       
  [5] XVector_0.30.0         base64enc_0.1-3        rstudioapi_0.13        listenv_0.8.0         
  [9] bit64_4.0.5            AnnotationDbi_1.52.0   prodlim_2019.11.13     fansi_0.5.0           
 [13] lubridate_1.8.0        codetools_0.2-18       splines_4.0.4          doParallel_1.0.16     
 [17] impute_1.64.0          cachem_1.0.6           knitr_1.36             geneplotter_1.68.0    
 [21] Formula_1.2-4          pROC_1.18.0            caret_6.0-90           annotate_1.68.0       
 [25] cluster_2.1.2          GO.db_3.12.1           png_0.1-7              pheatmap_1.0.12       
 [29] BiocManager_1.30.16    compiler_4.0.4         httr_1.4.2             backports_1.3.0       
 [33] assertthat_0.2.1       Matrix_1.3-4           fastmap_1.1.0          htmltools_0.5.2       
 [37] tools_4.0.4            gtable_0.3.0           glue_1.4.2             GenomeInfoDbData_1.2.4
 [41] reshape2_1.4.4         dplyr_1.0.7            Rcpp_1.0.7             vctrs_0.3.8           
 [45] preprocessCore_1.52.1  nlme_3.1-153           iterators_1.0.13       timeDate_3043.102     
 [49] xfun_0.28              gower_0.2.2            stringr_1.4.0          globals_0.14.0        
 [53] lifecycle_1.0.1        XML_3.99-0.8           future_1.23.0          zlibbioc_1.36.0       
 [57] MASS_7.3-54            scales_1.1.1           ipred_0.9-12           RColorBrewer_1.1-2    
 [61] memoise_2.0.0          gridExtra_2.3          ggplot2_3.3.5          rpart_4.1-15          
 [65] latticeExtra_0.6-29    stringi_1.7.5          RSQLite_2.2.8          genefilter_1.72.1     
 [69] foreach_1.5.1          checkmate_2.0.0        BiocParallel_1.24.1    lava_1.6.10           
 [73] rlang_0.4.12           pkgconfig_2.0.3        bitops_1.0-7           lattice_0.20-45       
 [77] purrr_0.3.4            htmlwidgets_1.5.4      recipes_0.1.17         bit_4.0.4             
 [81] tidyselect_1.1.1       parallelly_1.28.1      plyr_1.8.6             magrittr_2.0.1        
 [85] R6_2.5.1               generics_0.1.1         Hmisc_4.6-0            DelayedArray_0.16.3   
 [89] DBI_1.1.1              pillar_1.6.4           foreign_0.8-81         withr_2.4.2           
 [93] survival_3.2-13        RCurl_1.98-1.5         nnet_7.3-16            tibble_3.1.5          
 [97] future.apply_1.8.1     crayon_1.4.2           utf8_1.2.2             jpeg_0.1-9            
[101] locfit_1.5-9.4         grid_4.0.4             data.table_1.14.2      blob_1.2.2            
[105] ModelMetrics_1.2.2.2   digest_0.6.28          xtable_1.8-4           munsell_0.5.0
WGCNA • 1.7k views
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1
Entering edit mode

Length of 'xLabels' must equal the number of columns in 'Matrix. indicates that you provided more trait labels in names(design2) than how much it is present in colnames(moduleTraitCor).

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0
Entering edit mode

Thank you for your reply , The dim function shows that both have the same column number

dim(design2) [1] 20 3 dim(moduleTraitCor) [1] 113 3

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0
Entering edit mode

I resolved the issue by changing design2 into a data frame.

Many thanks.

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