**40**wrote:

I have a RNA-Seq time series with two conditions (SD and LD) and 3 time points (0, 2, and 4). There are three biological replicates per sample. I have used DESeq2 to do a likelihood ratio test on the following designs:

full ~ condition + time + condition:time reduced ~ condition + time

I understand that this tests for the effects of the two conditions on the pattern of expression which is what I want. Here are the names of my coefficients:

> resultsNames(dds_test) [1] "Intercept" "condition_LD_vs_SD" "time_2_vs_0" "time_4_vs_0" "conditionLD.time2" [6] "conditionLD.time4"

I would also like to contrast the difference between the conditions at the three time points and between time points within each condition. I was hoping someone could confirm my interpretations and answer a question about comparing time points which are not the baseline.

So am I correct in thinking I can test the difference between the conditions at the three timepoints like so:

results(dds_test, name="condition_LD_vs_SD", test="Wald") results(dds_test, contrast=list(c("condition_LD_vs_SD","conditionLD.time2")), test="Wald") results(dds_test, contrast=list(c("condition_LD_vs_SD","conditionLD.time4")), test="Wald")

and between time points within each condition like so:

- Condition SD

results(dds_test, contrast=list(c("time_2_vs_0")), test="Wald") results(dds_test, contrast=list(c("time_4_vs_0")), test="Wald")

- Condition LD

results(dds_test, contrast=list(c("time_2_vs_0", "conditionLD.time2")), test="Wald") results(dds_test, contrast=list(c("time_4_vs_0", "conditionLD.time4")), test="Wald")

Is this correct and is there an easy way to calculate and test the fold changes between time points 2 and 4?

This is my sample table:

sample condition time replicate LD_ZT4_1 LD_ZT4_1 LD 4 1 LD_ZT4_2 LD_ZT4_2 LD 4 2 LD_ZT4_3 LD_ZT4_3 LD 4 3 SD_ZT4_1 SD_ZT4_1 SD 4 1 SD_ZT4_2 SD_ZT4_2 SD 4 2 SD_ZT4_3 SD_ZT4_3 SD 4 3 SD_ZT0_1 SD_ZT0_1 SD 0 1 SD_ZT0_2 SD_ZT0_2 SD 0 2 SD_ZT0_3 SD_ZT0_3 SD 0 3 SD_ZT2_1 SD_ZT2_1 SD 2 1 SD_ZT2_2 SD_ZT2_2 SD 2 2 SD_ZT2_3 SD_ZT2_3 SD 2 3 LD_ZT0_1 LD_ZT0_1 LD 0 1 LD_ZT0_2 LD_ZT0_2 LD 0 2 LD_ZT0_3 LD_ZT0_3 LD 0 3 LD_ZT2_1 LD_ZT2_1 LD 2 1 LD_ZT2_2 LD_ZT2_2 LD 2 2 LD_ZT2_3 LD_ZT2_3 LD 2 3

**19k**• written 12 months ago by gtho123 •

**40**