gravatar for farid.zia

2 hours ago by

I've beed doing RNA-Seq analysis using R. However, when I get the final edgeR_result file, the logCPM values are very high which is not true for the genes I'm studying since they are extremely low expressed. I've checked my count table many times and no mistake there. Can someone help me please to figure it out why I'm getting those high values? Thanks
I also put the script I use in R in case needed:

cts <- read.csv("normCounts.txt", sep = 't', row.names = 1, header = FALSE) 
group <- (c(1,1,1,1,2,2,2,2))
cts <- DGEList(cts, group)
#cts <- calcNormFactors(y)
design <- model.matrix(~group)
cts <- estimateDisp(cts, design)
fit <- glmQLFit(cts, design)
qlf <- glmQLFTest(fit, coef = 2)
write.table(qlf$table, file = "edgeR_result.txt")
res <- qlf$table

ggplot(res, aes(x=logCPM, y=logFC, color=PValue < 0.05)) + 
    geom_point() + geom_rug(sides = "l") + theme_minimal()

fit2 <- glmFit(cts, design)

Source link