LRT test for different timepoints (one tissue types vs. many tissue types)
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@b6320868
Last seen 2 days ago
United States

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!

DESeq2 • 199 views
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@mikelove
Last seen 1 day ago
United States

No, this is a contrast of estimated coefficient (e.g. the Wald test).

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