''' getwd();

workingDir = ".";
setwd(workingDir); 

library(WGCNA);

options(stringsAsFactors = FALSE);

femData = read.csv("GSE78929_series_matrix (1).csv");

dim(femData);
names(femData);


datExpr0 = as.data.frame(t(femData[, -c]));
names(datExpr0) = femData$substanceBXH;
rownames(datExpr0) = names(femData)[-c];


gsg = goodSamplesGenes(datExpr0, verbose = 3);
gsg$allOK

'''

output

 datExpr0 = as.data.frame(t(femData[, -c]));
Error in -c : invalid argument to unary operator
> names(datExpr0) = femData$substanceBXH;
Error in names(datExpr0) = femData$substanceBXH : 
  object 'datExpr0' not found
> rownames(datExpr0) = names(femData)[-c];
Error in -c : invalid argument to unary operator
> gsg = goodSamplesGenes(datExpr0, verbose = 3);
 Flagging genes and samples with too many missing values...
  ..step 1
Error in as.matrix(datExpr) : object 'datExpr0' not found
> gsg$allOK
Error: object 'gsg' not found
> 

Hi, WGCNA is not a Bioconductor package. This forum was created to address technical issues pertaining to Bioconductor packages. Irrespective, please try to solve your first error (I have pasted it again below). Please debug in your own time, but by closely following the WGCNA tutorials.

Your first error, the issue relating specifically with -c. What are you hoping to do here? Are you supposed to have a variable named c? - poor choice, if so, as c is also a very common function name.

datExpr0 = as.data.frame(t(femData[, -c]));
Error in -c : invalid argument to unary operator

Kevin