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6 hours ago by

I am trying to use the DESeq2 package to compute differentially expressed genes from raw RNA-Seq counts, and I am having trouble setting up the design. I have 57 samples consisting of 2 diseases groups, 19 patients, and 3 tissue types. An example of my design:

Sample  Disease   Patient   Tissue
1       A         1         x
2       A         1         y
3       A         1         z
4       A         2         x
5       A         2         y
6       A         2         z
7       A         3         x
8       A         3         y
9       A         3         z
10      A         4         x
11      A         4         y
12      A         4         z
13      A         5         x
14      A         5         y
15      A         5         z
16      A         6         x
17      A         6         y
18      A         6         z
19      A         7         x
20      A         7         y
21      A         7         z
22      A         8         x
23      A         8         y
24      A         8         z
25      A         9         x
26      A         9         y
27      A         9         z
28      A         10        x
29      A         10        y
30      A         10        z
31      A         11        x
32      A         11        y
33      A         11        z
34      A         12        x
35      A         12        y
36      A         12        z
37      A         13        x
38      A         13        y
39      B         13        z
40      B         14        x
41      B         14        y
42      B         14        z
43      B         15        x
44      B         15        y
45      B         15        z
46      B         16        x
47      B         16        y
48      B         16        z
49      B         17        x
50      B         17        y
51      B         17        z
52      B         18        x
53      B         18        y
54      B         18        z
55      B         19        x
56      B         19        y
57      B         19        z

The comparisons of interest are pairwise comparisons between the interactions of Disease and Tissue (A.x vs A.y, A.x vs A.z, B.x vs. B.y, etc.) taking into account the pairing of the tissues by each patient. I also want to compare similar tissues across diseases (A.x vs B.x, A.y vs B.y) but without the pairing of course. I tried the following design in the DESeq2 workflow:

~Patient + Disease:Tissue

but I received the following error:

Error in checkFullRank(modelMatrix) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  Levels or combinations of levels without any samples have resulted in
  column(s) of zeros in the model matrix.

So I read the DESeq2 vignette and attempted their solution by creating a new variable for patients nested within groups:

Sample  Disease   Patient   Tissue   Patient.n
1       A         1         x        1
2       A         1         y        1
3       A         1         z        1
4       A         2         x        2
5       A         2         y        2
6       A         2         z        2
7       A         3         x        3
8       A         3         y        3
9       A         3         z        3
10      A         4         x        4
11      A         4         y        4
12      A         4         z        4
13      A         5         x        5
14      A         5         y        5
15      A         5         z        5
16      A         6         x        6
17      A         6         y        6
18      A         6         z        6
19      A         7         x        7
20      A         7         y        7
21      A         7         z        7
22      A         8         x        8
23      A         8         y        8
24      A         8         z        8
25      A         9         x        9
26      A         9         y        9
27      A         9         z        9
28      A         10        x        10
29      A         10        y        10
30      A         10        z        10
31      A         11        x        11
32      A         11        y        11
33      A         11        z        11
34      A         12        x        12
35      A         12        y        12
36      A         12        z        12
37      A         13        x        13
38      A         13        y        13
39      B         13        z        13
40      B         14        x        1
41      B         14        y        1
42      B         14        z        1
43      B         15        x        2
44      B         15        y        2
45      B         15        z        2
46      B         16        x        3
47      B         16        y        3
48      B         16        z        3
49      B         17        x        4
50      B         17        y        4
51      B         17        z        4
52      B         18        x        5
53      B         18        y        5
54      B         18        z        5
55      B         19        x        6
56      B         19        y        6
57      B         19        z        6

with the following suggested design:

~Disease + Disease:Patient.n + Disease:Tissue

But I get the same error as above. Not sure what I'm doing here, any help is appreciated.



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