how to make a group to apply the data to CAMERA
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Akira • 0
@72a4cfa2
Last seen 5 weeks ago
Japan

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
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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.

Best,

CAMERA • 113 views
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@gordon-smyth
Last seen 7 hours ago
WEHI, Melbourne, Australia

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.

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Thank you so much for your quick answer!! I will look into them! I appreciate your kind support.