Query regarding WGCNA module formation
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@6d5973d2
Last seen 10 days ago
India

I am trying to make a co-expression module with the following input gene-set associated standard division into a csv file and R-code but I'm getting error at the point of creating similarity matrix-

Geneid Standard_Deviation

TEA_015735 136871.105296187

TEA_021485 90055.8355925799

TEA_008699 52986.1997835285

TEA_006622 52363.8854613665

TEA_024055 46407.075185256

TEA_020597 33511.1751584453

TEA_028572 29998.4692072409

TEA_001699 27893.7930167468

TEA_001579 25183.9331177197

workingData = read.csv("gene_count_matrix _sd.csv", header = T, row.names =1)

cordist <- function(dat) { cor_matrix <- cor(t(dat))

dist_matrix <- as.matrix(dist(dat, diag=TRUE, upper=TRUE)) dist_matrix <- log1p(dist_matrix) dist_matrix <- 1 - (dist_matrix / max(dist_matrix))

sign(cor_matrix) * ((abs(cor_matrix) + dist_matrix)/ 2) }

sim_matrix <- cordist(workingData)

Error is following in R studio -

Error in cor(t(dat)) : 'x' has a zero dimension.

For reference, I Have installed the following libraries in R studio- WGCNA, knitr, reshape2, limma, gplots, ggplot2, RColorBrewer

WGCNA RNAseq RNASeqData • 143 views
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The cordist function fails on the first step. What is the dimensions of workingData: dim(workingData) ?

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