Hello,

I'm trying to design matrix so I can create combinations and extract the DEGs. I've been looking all over the web and I know how to create this matrix, however, when I create group as below

Group <- factor(c("Advshoot", "Cone",  "Gland", "Leaf", "Root", "Shoottip"))
Group <- relevel(Group, ref="Root")
design <- model.matrix(~0+Group)
colnames(design) <- levels(Group)

it has 6 tissues as I need it, while my y, library levels counts one of the tissues, Cone, as two

Levels: Advshoot Cone Cone  Gland Leaf Root Shoottip

so it sums up as 7 tissue types instead of 6 and running this

v <- voom(y,design,plot = TRUE)

gives this error

Error in lmFit(y, design, block = block, correlation = correlation, weights = weights) : 
  row dimension of design doesn't match column dimension of data object

Appreciate your help.

Thanks,

The Group factor needs to have an entry for each sample, not just an entry for each distinct tissue type. Please see the examples in the limma or edgeR documentation.

How many colums (i.e., samples) does your data have? Please show the output from:

class(y)
head(as.matrix(y))