Hello all,
I am using DESeq2 for the following analysis:
I have RNA-Seq data from 2 tissues and 4 time points, with 4 replicates for each condition. I have two tissues (liver and scn) and four timepoints (3,9,15,21).
I'm trying to test for genes where time is a factor, so my full model is
while my reduced is simply
Things look good, but when the results get returned, the model has compared each timepoint to time 3:
Since I'm looking for evidence of circadian regulation, time 3 isn't really a baseline starting point as in the fission data from the Bioconductor rnaseqGene workflow.
I'm thinking pairwise comparisons across time points might be better, even though the number of points is small (4).
I'd appreciate any help in building my model better.
Thanks!
-John
I am using DESeq2 for the following analysis:
I have RNA-Seq data from 2 tissues and 4 time points, with 4 replicates for each condition. I have two tissues (liver and scn) and four timepoints (3,9,15,21).
I'm trying to test for genes where time is a factor, so my full model is
Code:
~ tissue + time + tissue:time
Code:
~ tissue
Code:
> resultsNames(dds) [1] "Intercept" "tissue_scn_vs_liver" "time_9_vs_3" "time_15_vs_3" "time_21_vs_3" [6] "tissuescn.time9" "tissuescn.time15" "tissuescn.time21"
I'm thinking pairwise comparisons across time points might be better, even though the number of points is small (4).
I'd appreciate any help in building my model better.
Thanks!
-John
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