In edgeR, given the following data table:

GENE EXPRESSION DISEASE A B
A1BG  3       1   0   0
A1BG 0       1   0   0
...
ZZZ3   6       0   0   1
ZZZ3   7       0   0   1

A: concentration of compound A (continuous var)

B: concentration of compound B (continuous var)

DISEASE: 0/1 whether it's a disease or normal sample

If what I care is to do the following "glm":

EXPRESSION ~ intercept + DISEASE + A + B

Then,

1) How should I define "group" in edgeR? DISEASE can be grouped, but A or B cannot because they are continuous

2) coef = 3?

3) Should I use contrast of c(0, 1, 1, 1)?

In effect, I don't know much about "coef = x" or why one needs to "group" or specify "contrast". If we can assume EXPRESSION or log(EXPRESSION) is normally distributed, then in R we can simply do

glm(EXPRESSION ~ DISEASE + A + B)

Don't know why edgeR is so (unnecessarily?) complicated.

It would be much appreciated if someone could post the actual edgeR code, or just enlighten me with some teaching.

This is what I have come to so far:

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d<-read.table("myfile.txt", sep="\t", header=T);
sd<-subset(d, GENE=="A1BG");
attach(sd)
dsn<-model.matrix(~DISEASE+A+B, data=sd);
fit<-glmFit(EXPRESSION, dsn, coef=c(2,3,4))

-----------------------------------------------------------

And I got the following error:

-----------------------------------------------------------

> fit<-glmFit(EXPRESSION, dsn, coef=c(2,3,4))

Error in glmFit.default(EXPRESSION, dsn, coef = c(2, 3, 4)) : 

  No dispersion values provided.

-----------------------------------------------------------

coef=2 yielded the same error.

Thanks a lot in advance.

Those expression values aren't counts, so you shouldn't be using edgeR in the first place. And the A and B covariates aren't continuous, so far as I can tell. And you don't pass raw matrices to edgeR, which you would already know if you had read the edgeR User's Guide. Or the glmFit help page.

From what you have shown it doesn't look like you have even tried to understand what you are doing. You will find that it's hard to get people to help you when it seems you are unwilling to help yourself. You should at the very least read the edgeR User's Guide, which is quite comprehensive.