WGCNA R Dataframe using
1 answer
as.matrix
This is count data; so I would strongly recommend filtering it for low counts and normalizing it with limma
expr <- matrix(as.integer(your.df), nrow=nrow(your.df))
rownames(expr) <- rownames(your.df)
colnames(expr) <- colnames(your.df)
med.cnt <- apply(expr, 1, median)
expr.vm <- limma::voom(expr)$E
expr.vm <- expr.vm[med.cnt > 5,] # or so -- see how many genes there are and how stable your results are
expr.for.wgcna <- t(expr.vm) # WGCNA expects genes to be columns
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Show us your code and tell us what you've tried. Googling the error message should be enough to solve this problem.
What does
str(head(datExpr[,1:5])show? Also, you're reading intoDatExprand usingdatExprin the next line. Is that a typo or are they 2 different objects?it is a typo.
From your screenshot, I thought the gene IDs were rownames but you have them as a non-numeric column, which makes the error kinda obvious, don't you think?
Use
as.matrixon the dataframe after excluding the first column.