I just want to verify my code without replication using edgeR. Please check it and give your suggestions. it may help me to go forward. ***Thanks in advance***
library(edgeR)
rawpattihypo <- read.table("rawpattihypo", header = TRUE, row.names = 1)
colnames(rawpattihypo) <- gsub(".bam", "", colnames(rawpattihypo), fixed = T)
colnames(rawpattihypo) <- gsub(".bam", "", colnames(rawpattihypo), fixed = T)
colnames(rawpattihypo) <- gsub("..", "", colnames(rawpattihypo), fixed = T)
rawpattihypo <- rawpattihypo[ ,c(-1:-5)]
head(rawpattihypo)
condition <- factor(c("Bro","Lay"))
d <- DGEList(counts = rawpattihypo, group=condition)
head(d)
d1 <- calcNormFactors(d)
head(d1)
d1$samples
bcv <- 0.2
et <- exactTest(d1, dispersion = bcv^2)
top <- topTags(et)
head(top)
cpm(d1)[rownames(top), ]
summary(de <- decideTestsDGE(et))
detags <- rownames(d1)[as.logical(de)]
plotSmear(et, de.tags=detags)
abline(h=c(-1, 1), col="blue")
write.csv(et,"demo_edger.csv")