Entering edit mode
Shi, Tao
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720
@shi-tao-199
Last seen 8.8 years ago
Dear Jenny, Gordon, and the list,
This is a follow-up on the thread about handling nested design using
LIMMA posted last year (please see
https://stat.ethz.ch/pipermail/bioconductor/2006-February/012018.html
).
I have a data set which has very similar design like Jenny's. 6
animals, 3 in the control group and 3 in the treated group. 2
biological samples were taken from each animal and each was hybdized
to 2 arrays. All arrays have duplicate sets of probes (so there are 4
technical replicates for each biological samples).
After reading the posts by Jenny, Gordon and others, I'm a bit
confused with what should be the final approach for this kind of
design. I do agree with Jenny that the different biological samples
from the same animal (or in her case, different offsprings from the
same dam) should not be treated as technical replicates, so I'm not
quite sure about using duplicateCorrelation here. What I did is
first, summarized all the technical replicates (they are usually
highly correlated) to get one measurement for each biological samples,
then fitted LIMMA with a nested design model matrix (see below).
Is this OK and like to hear more comments. Thanks in advance.
...Tao
### after summarization of the technical replicates
> trt
[1] control control control control control control treat treat
treat treat treat treat
Levels: control treat
> animal
[1] 1 1 2 2 3 3 1 1 2 2 3 3
Levels: 1 2 3
>
> design.matrix <- model.matrix( ~ -1 +trt/animal)
> design.matrix
trtcontrol trttreat trtcontrol:animal2 trttreat:animal2
trtcontrol:animal3 trttreat:animal3
1 1 0 0 0
0 0
2 1 0 0 0
0 0
3 1 0 1 0
0 0
4 1 0 1 0
0 0
5 1 0 0 0
1 0
6 1 0 0 0
1 0
7 0 1 0 0
0 0
8 0 1 0 0
0 0
9 0 1 0 1
0 0
10 0 1 0 1
0 0
11 0 1 0 0
0 1
12 0 1 0 0
0 1
attr(,"assign")
[1] 1 1 2 2 2 2
attr(,"contrasts")
attr(,"contrasts")$trt
[1] "contr.treatment"
attr(,"contrasts")$animal
[1] "contr.treatment"
>
> fit <- lmFit(dat.temp, design=design.matrix)
....
contrast,
ebayes,
toptable,
.....
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