I am getting this error- "x must be numeric" when running this code. I am working on a pre processed data. The data frame is list.
#moderated t test using limma
file <- rma # Column 1 contains row-names
group <- rep(0:1, c(3,5))
library (limma)
lmFit(object, design=NULL, ndups=1, spacing=1, block=NULL, correlation, weights=NULL, method="ls", ...)
fit <- lmFit(file[-10, -1], design=group)
fit2 <- eBayes(fit)
toptableOut<- topTable(fit2, number=Inf, adjust.method="BH")$t
topTable(fit2, coef = 1, number = Inf, confint = TRUE, sort.by = "none")[,-4]
x <- cbind(file[,1],toptableOut)
write.table(x,"<filename>.txt", quote=F, row.names=FALSE, sep="\t")