[BioC] help with paired-test in limma
ariel.chernomoretz at crchul.ulaval.ca
Tue Jul 5 18:09:46 CEST 2005
This is my first time with limma (and also with linear models!).
After reading the vignettes, papers and previously posted messages I came out
with something, but I am not sure it is the correct procedure....in particular
I have doubts related to how to handle with limma the paired nature of my
design. I would greatly appreciate some remarks, comments, help, etc.
I want to study the differences between two treatments: allocationA and
allocationB, using single color affymetrix arrays, in a paired design.
Two samples were taken from 13 patients, one before, and the other after
treatment. There were 6 and 7 patients treated with allocationA, and
allocationB, respectively. Each sample was technically replicated, so at the
end we have 4 chip per patient.
The experimental setup looks like this:
Sample BeforeAfter Patient allocation
1 0 1 A
2 0 1 A
3 1 1 A
4 1 1 A
5 0 2 A
6 0 2 A
7 1 2 A
8 1 2 A
9 0 3 B
10 0 3 B
11 1 3 B
12 1 3 B
. . . .
. . . .
52 1 13 B
After reading some posts I decided to take the average of technical
replicates. Then I used a block in order to get the lmFit, and I calculated
the contrasts of interest:
> Interac =c(0,0,0,1))
I think that in this way I am implicitly assuming an intrablock correlation
level of 0.75. Is this somehow appropriate in order to consider this
a paired t-test like analysis?
With duplicateCorrelation, I get a value of 0.21 (!)
Is this value the one I should consider for lmFit ?
Using this rather low value isn't like disregarding
the before-after pairing for each patient? Shouldn't I tweak the correlation
level to an artificially higher value (for instance 0.9) instead?
Any comments would be highly appreciated
Ariel Chernomoretz, Ph.D.
Centre de recherche du CHUL
2705 Blv Laurier, bloc T-367
(418)-525-4444 ext 46339
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