I have a matrix of gene expression data for multiple samples from TCGA which I converted into a matrix from a GCT file.
# Convert to R dataype expr <- read.csv("BRCA_dataset2.gct", sep = "\t", header=FALSE) # Clean up the data expr <- expr[-2,] expr <- expr[-1,] expr <- janitor::row_to_names(expr, row_number = 1)
Next, I read in a list of genes for my gene set by doing the following
anti.apop <- read.delim(file.path("anti-apop singh.txt"))[, 1] #Convert to list object anti <- as.list(anti.apop)
Now when I try to run gsva, I am met with the following error
> gsva.out <- gsva(expr, anti) Error in .local(expr, gset.idx.list, ...) : Less than two genes in the input expression data matrix In addition: There were 50 or more warnings (use warnings() to see the first 50)
Why does it say there are less than two genes in the expression data matrix? I went through and searched for the genes in the gene list in the expression matrix and they are all there. Why isn't GSVA recognizing it?