Create design & contrast matrix for differential state analy
I have a mass cytometry dataset of samples collected from patients with AML (n=30). There is one sample from each patient, and the patients can be divided into two groups based on initial response to experimental therapy (21 responders vs 9 non-responders). I have been using the CATALYST pipeline and the diffcyt() function to do differential state analysis. Using this I find lot if very significant differences between the groups. But when I use a different script that just do a lot of two sided T-tests (and then FDR adjustment), I find nothing significant.
When I use diffcyt() and my t-test script on a different and paired dataset, they find similar significant differences. So, I surmise that my design and/or contrast is not correctly set up? Can anyone help me? I hope my R output below is helpful, and that this is a suitable forum to ask for help
> design <- createDesign(ei(sce), cols_design = “condition”)
(Intercept) conditionRD
1 1 1
2 1 1
3 1 0
4 1 1
5 1 0
6 1 0
7 1 0
8 1 0
9 1 0
10 1 0
11 1 0
12 1 0
13 1 0
14 1 0
15 1 0
16 1 1
17 1 1
18 1 1
19 1 0
20 1 1
21 1 0
22 1 1
23 1 1
24 1 0
25 1 0
26 1 0
27 1 0
28 1 0
29 1 0
30 1 0
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$condition
[1] "contr.treatment"
> contrast <- createContrast(c(0,1))
[,1]
[1,] 0
[2,] 1
When I use diffcyt() and my t-test script on a different and paired dataset, they find similar significant differences. So, I surmise that my design and/or contrast is not correctly set up? Can anyone help me? I hope my R output below is helpful, and that this is a suitable forum to ask for help
> design <- createDesign(ei(sce), cols_design = “condition”)
(Intercept) conditionRD
1 1 1
2 1 1
3 1 0
4 1 1
5 1 0
6 1 0
7 1 0
8 1 0
9 1 0
10 1 0
11 1 0
12 1 0
13 1 0
14 1 0
15 1 0
16 1 1
17 1 1
18 1 1
19 1 0
20 1 1
21 1 0
22 1 1
23 1 1
24 1 0
25 1 0
26 1 0
27 1 0
28 1 0
29 1 0
30 1 0
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$condition
[1] "contr.treatment"
> contrast <- createContrast(c(0,1))
[,1]
[1,] 0
[2,] 1