Here is what I am doing, after creating the design matrix, I am trying to create the contrast matrix

# > sample <- factor(rep(c("Non neoplastic","Tumor"), each=21))
> design.mat <- model.matrix(~0+sample)
> colnames(design.mat) <- levels(sample)
> design.mat
   Non neoplastic Tumor
1               1     0
2               1     0
3               1     0
4               1     0
5               1     0
6               1     0
7               1     0
8               1     0
9               1     0
10              1     0
11              1     0
12              1     0
13              1     0
14              1     0
15              1     0
16              1     0
17              1     0
18              1     0
19              1     0
20              1     0
21              1     0
22              0     1
23              0     1
24              0     1
25              0     1
26              0     1
27              0     1
28              0     1
29              0     1
30              0     1
31              0     1
32              0     1
33              0     1
34              0     1
35              0     1
36              0     1
37              0     1
38              0     1
39              0     1
40              0     1
41              0     1
42              0     1
attr(,"assign")
[1] 1 1
attr(,"contrasts")
attr(,"contrasts")$sample
[1] "contr.treatment"

> contrast.mat <- makeContrasts(diff = "Non neoplastic-Tumor", levels = design.mat)

#Error in makeContrasts(diff = "Non neoplastic - Tumor", levels = design.mat) : 
  The levels must by syntactically valid names in R

You cannot use a syntactically invalid name with makeContrasts. In your case, the problem is that you have a space, and R doesn't recognize that Non and neoplastic are intended to go together. Normally R would run that sort of thing through make.names to make it syntactically valid (for example as a column name for a data.frame), but the expectation for makeContrasts is that you already have that.

> make.names("Non neoplastic")
[1] "Non.neoplastic"

So one thing you could do is change it to Non.neoplastic. Or Non_neoplastic, or NonNeoplastic. You get the idea.