Entering edit mode
4.0 years ago
jimmy0958073736
▴
40
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??
Oh, that's right. I missed that. THX
Dear Mark,
I have the same issue even providing the "designmatrix". I have only one sample for each condition and use the approach below:
I get "Need at least two columns for design, usually the first is the intercept column" error in
lrt <- glmLRT(fit)
step. I have tried a lot and do not know how to fix it - could you please help me with this? Thank you.Like I said above please read the manual. It's impossible to do DE with 1 sample in each condition. You need at minimum 2 samples per condition.
Please read the manual.