EdgeR without replication
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@7ca586f4
Last seen 9 weeks ago
India

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")

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