Hi so I'm trying to do limma fitting on my data but i keep getting the following error

> library(limma)
> data<-read.table("C:/Users/test/Desktop/book1.txt",header = T, row.names = 1)
> dim(data)
[1] 720  14
> pairs(data)
> pairs(data)# it is better to use log2
> design <- model.matrix(~ 0+factor(c(rep(1,6),rep(2,8))))
> colnames(design) <- c("treat1","control1")
> #fit a linear model
>  fit <- lmFit(data, design)
Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric

You would have to show what is in your 'data' object (btw, not a really good name, as you are masking an existing function). But do note that getEAWP(), which is the function that processes your data will do this:

y$exprs <- as.matrix(object)

and if any of the values in your data.frame are factors (the default for read.table() is to convert character like data into factors), then you will end up with a matrix of all characters. To wit:

> z <- data.frame(1:10, 2:11)
> as.matrix(z)
      X1.10 X2.11
 [1,]     1     2
 [2,]     2     3
 [3,]     3     4
 [4,]     4     5
 [5,]     5     6
 [6,]     6     7
 [7,]     7     8
 [8,]     8     9
 [9,]     9    10
[10,]    10    11
> z <- data.frame(letters[1:10], z)
> as.matrix(z)
      letters.1.10. X1.10 X2.11
 [1,] "a"           " 1"  " 2"
 [2,] "b"           " 2"  " 3"
 [3,] "c"           " 3"  " 4"
 [4,] "d"           " 4"  " 5"
 [5,] "e"           " 5"  " 6"
 [6,] "f"           " 6"  " 7"
 [7,] "g"           " 7"  " 8"
 [8,] "h"           " 8"  " 9"
 [9,] "i"           " 9"  "10"
[10,] "j"           "10"  "11"
> z[,1]
 [1] a b c d e f g h i j
Levels: a b c d e f g h i j