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I am performing WGCNA analysis on my RNAseq dataset for the first time and getting this error message:
> net = blockwiseModules(expression, power = 6,
+ TOMType = "unsigned", minModuleSize = 30,
+ reassignThreshold = 0, mergeCutHeight = 0.25,
+ numericLabels = TRUE, pamRespectsDendro = FALSE,
+ saveTOMs = TRUE,
+ saveTOMFileBase = "SW_TOM",
+ verbose = 3)
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
..Excluding 722 genes from the calculation due to too many missing samples or zero variance.
..step 2
....pre-clustering genes to determine blocks..
Projective K-means:
..k-means clustering..
..merging smaller clusters...
Block sizes:
gBlocks
1 2 3 4 5
4999 4998 4945 4424 4306
..Working on block 1 .
Error in blockwiseModules(expression, power = 6, TOMType = "unsigned", :
REAL() can only be applied to a 'numeric', not a 'integer'
`
The code I used is given below. How do I solve this error?
library(WGCNA)
#Setting string not as factor
options(stringsAsFactors = FALSE)
#Enable multithread
enableWGCNAThreads()
#Reading the raw data (rows are the sample and columns the genes)
SWexpressiondata = read.csv("edgeR_normalized.csv")
#Create a new format expression data - remove gene name column
expression = as.data.frame(expressiondata[, -c(1)])
expression = t(expression)
#Column 1 - gene names
colnames(expression) = expressiondata$genes
rownames(expression) = names(expressiondata)[-c(1)]
#Group data in a dendogram to check outliers
sampleTree = hclust(dist(expression), method = "average")
dev.off()
sizeGrWindow(12,9)
par(cex = 0.6)
par(mar = c(0,4,2,0))
plot(sampleTree, main = "Sample clustering to detect outliers", sub="", xlab="", cex.lab = 1.5,
cex.axis = 1.5, cex.main = 2)
# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to = 20, by = 2))
# Call the network topology analysis function
sft = pickSoftThreshold(expression, # <= Input data
#blockSize = 30,
powerVector = powers,
verbose = 5)
# Plot the results:
sizeGrWindow(9, 5)
par(mfrow = c(1,2));
cex1 = 0.9;
# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[, 1],
-sign(sft$fitIndices[, 3]) * sft$fitIndices[, 2],
xlab = "Soft Threshold (power)",
ylab = "Scale Free Topology Model Fit, signed R^2",type="n",
main = paste("Scale independence"))
text(sft$fitIndices[, 1],
-sign(sft$fitIndices[, 3]) * sft$fitIndices[, 2],
labels = powers, cex = cex1, col = "red")
# this line corresponds to using an R^2 cut-off of h
abline(h = 0.90, col = "red")
# Mean connectivity as a function of the soft-thresholding power
plot(sft$fitIndices[, 1],
sft$fitIndices[, 5],
xlab = "Soft Threshold (power)",
ylab = "Mean Connectivity",
type = "n",
main = paste("Mean connectivity"))
text(sft$fitIndices[, 1],
sft$fitIndices[, 5],
labels = powers,
cex = cex1, col = "red")
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
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
[9] base
other attached packages:
[1] magrittr_2.0.1 edgeR_3.28.1 limma_3.42.2
[4] WGCNA_1.70-3 fastcluster_1.2.3 dynamicTreeCut_1.63-1
[7] ggplot2_3.3.5 org.Mm.eg.db_3.10.0 AnnotationDbi_1.48.0
[10] IRanges_2.20.2 S4Vectors_0.24.4 Biobase_2.46.0
[13] BiocGenerics_0.32.0 DOSE_3.12.0 clusterProfiler_3.14.3
[16] dplyr_1.0.7
loaded via a namespace (and not attached):
[1] fgsea_1.12.0 colorspace_2.0-2 ellipsis_0.3.2
[4] ggridges_0.5.3 qvalue_2.18.0 htmlTable_2.2.1
[7] base64enc_0.1-3 rstudioapi_0.13 farver_2.1.0
[10] urltools_1.7.3 graphlayouts_0.7.1 ggrepel_0.9.1
[13] bit64_4.0.5 fansi_0.5.0 xml2_1.3.2
[16] codetools_0.2-18 splines_3.6.3 doParallel_1.0.16
[19] impute_1.60.0 cachem_1.0.5 GOSemSim_2.12.1
[22] knitr_1.33 polyclip_1.10-0 Formula_1.2-4
[25] jsonlite_1.7.2 cluster_2.1.2 GO.db_3.10.0
[28] png_0.1-7 ggforce_0.3.3 BiocManager_1.30.16
[31] compiler_3.6.3 httr_1.4.2 backports_1.2.1
[34] rvcheck_0.1.8 assertthat_0.2.1 Matrix_1.3-4
[37] fastmap_1.1.0 tweenr_1.0.2 htmltools_0.5.1.1
[40] prettyunits_1.1.1 tools_3.6.3 igraph_1.2.6
[43] gtable_0.3.0 glue_1.4.2 reshape2_1.4.4
[46] DO.db_2.9 fastmatch_1.1-0 Rcpp_1.0.7
[49] enrichplot_1.6.1 vctrs_0.3.8 preprocessCore_1.48.0
[52] iterators_1.0.13 ggraph_2.0.5 xfun_0.24
[55] stringr_1.4.0 lifecycle_1.0.0 europepmc_0.4
[58] MASS_7.3-54 scales_1.1.1 tidygraph_1.2.0
[61] hms_1.1.0 RColorBrewer_1.1-2 memoise_2.0.0
[64] gridExtra_2.3 triebeard_0.3.0 rpart_4.1-15
[67] latticeExtra_0.6-29 stringi_1.7.2 RSQLite_2.2.7
[70] foreach_1.5.1 checkmate_2.0.0 BiocParallel_1.20.1
[73] rlang_0.4.11 pkgconfig_2.0.3 matrixStats_0.59.0
[76] lattice_0.20-41 purrr_0.3.4 htmlwidgets_1.5.3
[79] labeling_0.4.2 cowplot_1.1.1 bit_4.0.4
[82] tidyselect_1.1.1 plyr_1.8.6 R6_2.5.0
[85] generics_0.1.0 Hmisc_4.5-0 DBI_1.1.1
[88] pillar_1.6.1 foreign_0.8-75 withr_2.4.2
[91] survival_3.2-11 nnet_7.3-16 tibble_3.1.2
[94] crayon_1.4.1 utf8_1.2.1 viridis_0.6.1
[97] jpeg_0.1-8.1 progress_1.2.2 locfit_1.5-9.4
[100] grid_3.6.3 data.table_1.14.2 blob_1.2.1
[103] digest_0.6.27 tidyr_1.1.3 gridGraphics_0.5-1
[106] munsell_0.5.0 viridisLite_0.4.0 ggplotify_0.0.7