Entering edit mode
6.1 years ago
Gabby
▴
20
HI! I am trying to analyse Time course data with just one type cell (3 biological replicate ) for each point . I want to compare gene expression based on time point i.e time 1 with time 2 and so on (no treatment comparision at different points, becuase it's one type only).
So what I prepared so far is following and want to know, if I am on right path or not.
pData
minute replicate
r1d0 1 1
r1d1 2 1
r1d2 3 1
r2d0 1 2
r2d1 2 2
r2d2 3 2
r3d0 1 3
r3d1 2 3
r3d2 3 3
r3d3 4 3
dge <- DGEList(counts=exprs(mydata), group=pData(mydata)$minute)
design.mat <- model.matrix(~ 0 + dge$samples$group)
design.mat
colnames(design.mat) <-c("t0","t1","t2","t3","t4","t5","t6","t7","t8")
row.names(design.mat) <- colnames(dge)
# design.mat
# t0 t1 t2
#r1d0 1 0 0
#r1d1 0 1 0
#r1d2 0 0 1
#r2d0 1 0 0
#r2d1 0 1 0
#r2d2 0 0 1
#r3d0 1 0 0
#r3d1 0 1 0
#r3d2 0 0 1
dge = estimateCommonDisp(dge, verbose=TRUE)
dge <- estimateGLMCommonDisp(dge, design.mat)
dge <- estimateGLMTrendedDisp(dge, design.mat, method="power")
dge<- estimateGLMTagwiseDisp(dge,design.mat)
fit.edgeR <- glmFit(dge, design.mat)
contrasts.edgeR <- makeContrasts(t0-t4, levels=design.mat)
lrt.edgeR <- glmLRT(fit.edgeR, contrast=contrasts.edgeR)
I really need to know, if it's correct. what I am doing. Is there anyother tool? which is more better than this.
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