Question: Repeated measurements wtih limma
0
gravatar for Gurkenkönig
11 months ago by
Gurkenkönig0 wrote:

I have EPIC array methylation data and would like to check for differential methylation.

+------+-----+
| time | id  |
+------+-----+
| t0   | P1  |
+------+-----+
| t1   | P1  |
+------+-----+
| t0   | P2  |
+------+-----+
| t1   | P2  |
+------+-----+
| ...  | ... |
+------+-----+

So far I have always used the limma package in R here, but I have problems defining the study design for the repeated measures.

group <- factor(targets$time,levels=c("t0", "t1"))
id <- factor(targets$id)
design <- model.matrix(~id + group)

Can someone help me define the design correctly or point me in the right direction if the approach is completely wrong?

limma limma design matrix • 181 views
ADD COMMENTlink modified 11 months ago by Aaron Lun24k • written 11 months ago by Gurkenkönig0
Answer: Repeated measurements wtih limma
1
gravatar for Aaron Lun
11 months ago by
Aaron Lun24k
Cambridge, United Kingdom
Aaron Lun24k wrote:

Looks good to me. The last coefficient in design should represent the log-fold change (or for methylation data, the difference between M-values) between t0 and t1, which is presumably the contrast of interest here.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Aaron Lun24k
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