RNA-Seq T24,T1,T0 analysis

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

resultsNames(dds)

[1] "Intercept"              "Cell_line_U343_vs_U251" "Time_T1_vs_T0"          "Time_T24_vs_T0"        
[5] "Cell_lineU343.TimeT1"   "Cell_lineU343.TimeT24" 

U251: T1 Vs T0

U251.res.T1vsT0 <- results(dds, contrast=c('Time', 'T1', 'T0'))
U251.res.T1vsT0.sig <- U251.res.T1vsT0[order(U251.res.T1vsT0$padj),]
as.data.frame(U251.res.T1vsT0.sig)

U251: T24 Vs T0

U251.res.T24vsT0 <- results(dds, contrast=c('Time', 'T24', 'T0'))
## ALTERNATIVEly: results(dds, name="Time_T24_vs_T0")
U251.res.T24vsT0 <- U251.res.T24vsT0[order(U251.res.T24vsT0$padj),]
U251.res.T24vsT0.sig <- subset(U251.res.T24vsT0, padj<0.05)
as.data.frame(U251.res.T24vsT0.sig)

U343: T1 Vs T0

# sum of the base term + interaction term
U343.res.T1vsT0 <- results(dds, contrast=list(c("Time_T1_vs_T0","Cell_lineU343.TimeT1")))
U343.res.T1vsT0 <- U343.res.T1vsT0[order(U343.res.T1vsT0$padj),]
U343.res.T1vsT0.sig <- subset(U343.res.T1vsT0, padj<0.05)
as.data.frame(U343.res.T1vsT0.sig)

U343: T24 Vs T0

U343.res.T24vsT0 <- results(dds, contrast=list(c("Time_T24_vs_T0","Cell_lineU343.TimeT24")))
U343.res.T24vsT0 <- U343.res.T24vsT0[order(U343.res.T24vsT0$padj),]
U343.res.T24vsT0.sig <- subset(U343.res.T24vsT0, padj<0.05)
as.data.frame(U343.res.T24vsT0.sig)

Are U343 vs U251 changes different at T1 than at T0

Interpretation: Genes behaving similar between both groups at all time except between T1 and T0.

U343_vs_U251.T1vsT0 <- results(dds, name="Cell_lineU343.TimeT1")
U343_vs_U251.T1vsT0 <- U343_vs_U251.T1vsT0[order(U343_vs_U251.T1vsT0$padj),]
U343_vs_U251.T1vsT0.sig <- subset(U343_vs_U251.T1vsT0, padj<0.05)
as.data.frame(U343_vs_U251.T1vsT0.sig)

Are U343 vs U251 changes different at T24 than at T0

Interpretation: Genes behaving similar between both groups at all time except between T24 and T0.

U343_vs_U251.T24vsT0 <- results(dds, name="Cell_lineU343.TimeT24")
U343_vs_U251.T24vsT0 <- U343_vs_U251.T24vsT0[order(U343_vs_U251.T24vsT0$padj),]
U343_vs_U251.T24vsT0.sig <- subset(U343_vs_U251.T24vsT0, padj<0.05)
as.data.frame(U343_vs_U251.T24vsT0.sig)