Hi everyone, I did edgeR to analyze no replicated sample with the following code.
Unfortunately, I met some of the problems that I can't fix.
count <- read.table("D:/NDM-12-4/test/Vero.CH.CH-C100.normalisedReadCounts.txt", sep = "t", header = T, row.names = 1) view(count) d1 <- estimateGLMCommonDisp(count, design=NULL, verbose=TRUE) d2 <- estimateCommonDisp(count, verbose=TRUE) fit <- glmFit(count,dispersion = 0.26664) results <- glmLRT(fit, coef=2)
The result shows that
Error in glmLRT(fit, coef = 2) : Need at least two columns for design, usually the first is the intercept column
But actually, I put two samples inside the count file. So what does that mean??