Hi,

I have 2 groups, 4 samples per group, and I loaded the matrix after CuffDiff, as shown below.

NAME    Description                  high1  high2   high3   high4   low1            low2    low3    low4
A1BG    alpha-1-B glycoprotein  4.593   9.191   9.076   8.662   4.869   3.955   3.218   9.403
A1BG-AS1    A1BG antisense RNA 1    0.803   0.419   0   0.145   0           0.291   0           0
A1CF    APOBEC1 complementation factor  0.007   0.04    0   0           0           0           0           0.004
.
.
.

# GCT_data <- read.gct("data.gct.txt")

I also loaded the human c7 gene sets with this code

# load("human_c7_v5p2.rdata") MSig

After this, I want to run CAMERA, but I don't know how I can make a group to compare between high -vs low group. high group means high1, high2, high3, high4 low group means low1, low2, low3, low4.

I appreciate your kind help.

Best,

See the limma User's Guide for how to undertake differential expression analyses, including camera().

Alternatively, here is a complete workflow example.

By the way, CuffDiff is not considered a current software tool. You might consider revisiting the quantification pipeline as well.