Hello,

I performed a RNAseq experiment from microbial cultivations in order to investigate carbon catabolite repression.

I used 2 different strains: A and B

in 2 different media conditions and in a Mix of these conditions: x, y and xy

Experiments were performed in triplicates. Here is the experimental setup:

strain condition

`[1,] "A" "x" `

[2,] "A" "x"

[3,] "A" "x"

[4,] "A" "y"

[5,] "A" "y"

[6,] "A" "y"

[7,] "A" "xy"

[8,] "A" "xy"

[9,] "A" "xy"

[10,] "B" "x"

[11,] "B" "x"

[12,] "B" "x"

[13,] "B" "y"

[14,] "B" "y"

[15,] "B" "y"

[16,] "B" "xy"

[17,] "B" "xy"

[18,] "B" "xy"

Now iam trying to setup a model matrix.

Since I dont know if the media conditions have the same effect on the two strains, I want to include an interaction term strain:condition.

Now Iam not sure how to set a proper model which also takes the "Mixed" property of "xy" into account.

Should i treat it like a third condition (like "z") ?

If I would only have condition "x" and "y", I would set up the modelmatrix like this:

`strain <- factor(c("A", "A", "A", "A", "A", "A", "B", "B", "B", "B", "B", "B"))`

condition <- factor(c("x", "x", "x", "y", "y", "y", "x", "x", "x", "y", "y", "y"))

design <- model.matrix( ~ strain + condition + strain:condition)

> design

(Intercept) strainB conditiony strainB:conditiony

1 1 0 0 0

2 1 0 0 0

3 1 0 0 0

4 1 0 1 0

5 1 0 1 0

6 1 0 1 0

7 1 1 0 0

8 1 1 0 0

9 1 1 0 0

10 1 1 1 1

11 1 1 1 1

12 1 1 1 1

attr(,"assign")

[1] 0 1 2 3

attr(,"contrasts")

attr(,"contrasts")$strain

[1] "contr.treatment"

attr(,"contrasts")$condition

[1] "contr.treatment"

If you have any suggestions I would be very happy.

Best