Closed:Limma contrasts in Time series analysis

Question

[anoopta88]

Hi, I want to find out genes which are up-regulated or down-regulated over a period of time from RNASeq data. We have samples collected at 24, 48, 72 hours post infection. We do not have control samples. The objective is to find genes significantly over time in response to infection. I have used Limma, and the code used is given below, I want to confirm whether I am going in the correct direction.

data=read.delim("count.txt",header = T,row.names = 1,check.names = FALSE)

head(data)
 <- c(rep("Sample1", 3),
           rep("Sample2", 3),
           rep("Sample3", 3))

time.grp <- rep(c(24, 48, 72), 3)

groups <- as.factor(assay)

design <- model.matrix( ~0 + groups + time.grp)

fit <- lmFit(data, design)

cont.matrix <- makeContrasts(
  time = "time.grp",
  levels = design
)

fit.cont <- contrasts.fit(fit, cont.matrix)

efit.cont <- eBayes(fit.cont)

top_table <- topTable(efit.cont, adjust="fdr", n = Inf)