**0**wrote:

I am trying to set up model where I have paired biological replicates as a blocking factor, and I am interested in the differential expression in individual strains as well as between specific groups of strains that were isolated from similar environments. I am getting the Matrix not of full rank error even though none of the columns in my design matrix are all 0s. Any advice on how to resolve this problem?

After reading in my data, I made the following variables:

rep <- factor(c(1,2,1,2,1,2,1,2,1,2,1,2))

group <- factor(c(1,1,1,1,2,2,2,2,3,3,3,3))

strain <- factor(c(1,1,2,2,3,3,4,4,5,5,6,6))

I then created by design:

design <- model.matrix(~rep+group+strain, data=data)

which looks like this:

> design

(Intercept) rep2 group2 group3 strain2 strain3 strain4 strain5 strain6

1 1 0 0 0 0 0 0 0 0

2 1 1 0 0 0 0 0 0 0

3 1 0 0 0 1 0 0 0 0

4 1 1 0 0 1 0 0 0 0

5 1 0 1 0 0 1 0 0 0

6 1 1 1 0 0 1 0 0 0

7 1 0 1 0 0 0 1 0 0

8 1 1 1 0 0 0 1 0 0

9 1 0 0 1 0 0 0 1 0

10 1 1 0 1 0 0 0 1 0

11 1 0 0 1 0 0 0 0 1

12 1 1 0 1 0 0 0 0 1

attr(,"assign")

[1] 0 1 2 2 3 3 3 3 3

attr(,"contrasts")

attr(,"contrasts")$rep

[1] "contr.treatment"

attr(,"contrasts")$group

[1] "contr.treatment"

attr(,"contrasts")$strain

[1] "contr.treatment"

I then made my DGEList, normalized, and got an error while trying to estimate Dispersion.

y <- DGEList(counts=data[,1:12], group=group:strain:rep)

y<-calcNormFactors(y)

y <- estimateGLMCommonDisp(y,design)

> y <- estimateGLMCommonDisp(y,design)

Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset, :

Design matrix not of full rank. The following coefficients not estimable:

strain4 strain6

I also tried changing the order of variables in the model (~rep+strain+group) which results in the same error with group 2 and group 3 coefficients not estimable.

**36k**• written 3.6 years ago by kjclowers •

**0**