Entering edit mode
Hello,
I am hoping to get some guidance on how to perform LRT time point test on one tissue type vs average of several other tissue types.
I have an experiment design as follows:
Sample Tissue Timepoint
1 T1 1
2 T1 1
3 T1 1
4 T1 2
5 T1 2
6 T1 2
7 T2 1
8 T2 1
9 T2 1
10 T2 2
11 T2 2
12 T2 2
13 T3 1
14 T3 1
15 T3 1
16 T3 2
17 T3 2
18 T3 2
19 T4 1
20 T4 1
21 T4 1
22 T4 2
23 T4 2
24 T4 2
If it's just one condition, to compare T1 vs average of T2,T3,and T4,I know we can do something like:
res <- results(dds, contrast=c(1, -1/3, -1/3, -1/3))
For LRT, I can do:
dds <- DESeqDataSetFromMatrix(UMI_Count, ~ Tissue + Timepoint+ Tissue :Timepoint)
dds <- DESeq(dds, test="LRT", reduced = ~ Tissue + Timepoint)
resDDS <- results(dds)
Is there a easy way that I can combine both analysis to study Tissue :Timepoint interaction for tissue1 vs average all other tissue types.
Thanks!