Hi,
I am performing differential editing analysis using edgeR to identify differentially edited sites using the procedure for differentially methylated analysis (section 4.8 edgeRvignette). However, I have same patients sampled at three different conditions T0, T36, and T56 (paired design). Therefore, I used the below design
design <- model. Matrix(~0+ sample_id + time_point, data = colData)
(The goal is to find differentially edited sites T36 and T56 compared to T0 respectively) (vignette section 4.1)
This is what the colnames for my design look like
[1] "sample_id5039" "sample_id5124" "sample_id5152" "sample_id5156" "sample_id5316" [6] "sample_id5412" "sample_id5743" "sample_id5894" "sample_id6207" "sample_id6250" [11] "sample_id6453" "sample_id6582" "sample_id6599" "sample_id6636" "sample_id6663" [16] "sample_id6911" "sample_id7030" "sample_id7160" "sample_id7247" "sample_id7252" [21] "sample_id7577" "sample_id7589" "sample_id7647" "sample_id7683" "sample_id7733" [26] "sample_id7893" "sample_id8015" "sample_id8359" "sample_id8360" "sample_id8610" [31] "sample_id8640" "sample_id8656" "sample_id8968" "sample_id9088" "sample_id9140" [36] "sample_id9192" "sample_id9198" "sample_id9247" "sample_id9249" "sample_id9373" [41] "sample_id9388" "sample_id9415" "sample_id9918" "sample_id9943" "sample_id9997" [46] "time_pointT36" "time_pointT56"
I would like to set contrast between "time_pointT36 - time_pointT0" and 'time_pointT56-time_pointT0"
However, I am unsure how to do that.
I understand this is some overlook from my end but would really appreciate any help or pointers.
Thanks,
