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help > RE: Design matrix
Dec 16, 2017 05:12 AM | Andrew Zalesky
RE: Design matrix
Hi Alexia,
If you have missing time points for just a few subjects, I suggest excluding these subjects. Other methods can also be used to deal with missing data points.
The F test contrast of [0 0 1 1] is not comparing T1 vs T2. It will compare T1 vs T2 vs T3. Specifically, it will test the null hypothesis of T1 = T2 = T3. The null will be rejected and a significant result returned when any of the three time points are different (not just T1 or T2).
Given that you only have controls scanned at one time point, I don't think your 2nd design matrix is correct. For example, what is the difference between C1T1 and C1T2? It seems you are making this design too complicated. You need to first define the null hypothesis that you want to test when you introduce the controls into the design. You could simply test for patient control difference at each of the three time points. I.e. run three identical analyses at each of the three time points.
Andrew
Originally posted by Alexia Bourgeois:
If you have missing time points for just a few subjects, I suggest excluding these subjects. Other methods can also be used to deal with missing data points.
The F test contrast of [0 0 1 1] is not comparing T1 vs T2. It will compare T1 vs T2 vs T3. Specifically, it will test the null hypothesis of T1 = T2 = T3. The null will be rejected and a significant result returned when any of the three time points are different (not just T1 or T2).
Given that you only have controls scanned at one time point, I don't think your 2nd design matrix is correct. For example, what is the difference between C1T1 and C1T2? It seems you are making this design too complicated. You need to first define the null hypothesis that you want to test when you introduce the controls into the design. You could simply test for patient control difference at each of the three time points. I.e. run three identical analyses at each of the three time points.
Andrew
Originally posted by Alexia Bourgeois:
Hi Andrew,
I'm just beginning with NBS. I went through the forum and the manual but I'm still confused regarding the design matrix.
I have two groups of subject: one group of stroke patients scanned 3 times (Time Point 1, 2, 3) and 1 group of controls scanned only once (TP1).
I would like to compare the 3 time points across my group of patients, I guess this correspond to one-way ANOVA within subject analysis.
In this case, should I create the following matrice, here presented for two subjects: (P for patients, T for time point)
P1T1 1 0 1 0
P2T1 0 1 1 0
P1T2 1 0 0 1
P2T2 0 1 0 1
P1T3 1 0 0 0
P2T3 0 1 0 0
Echange block: [1 2 1 2 1 2]
Contrast F test [0 0 1 1] to compare here T1 vs T2?
Also Time point 1 and TP 3 are missing for two different patients. Should I remove these patients for this analysis?
Then to compare patients vs controls, I guess I have to select paired of time points to obtain a 2x2 model.
In this case I obtain this matrix (C for control, P for patients, T for Time point)
C1T1 0 1 1 0 0 0
C1T2 1 0 1 0 0 0
C2T1 0 1 0 1 0 0
C2T2 1 0 0 1 0 0
P1T1 0 0 0 0 1 0
P1T2 1 1 0 0 1 0
P2T1 0 0 0 0 0 1
P2T2 1 1 0 0 0 1
The 1st column correspond to the main effect of time -> F test - Contrast=[1 0 0 0 0 0] - Exchange blocks=[1 1 2 2 3 3 4 4]
The 2nd column correspond to the interaction between group x time -> t-test - Contrast=[0 -1 0 0 0 0] or [0 -1 0 0 0 0] - Exchange blocks=[1 1 2 2 3 3 4 4]
The fourth last columns correspond to the subject means. Should we automatically include it in the design matrix? What does it change?
Sorry for this long email but I'm quite lost! Thanks a lot in advance for your help and insights!
Regards,
Alexia
I'm just beginning with NBS. I went through the forum and the manual but I'm still confused regarding the design matrix.
I have two groups of subject: one group of stroke patients scanned 3 times (Time Point 1, 2, 3) and 1 group of controls scanned only once (TP1).
I would like to compare the 3 time points across my group of patients, I guess this correspond to one-way ANOVA within subject analysis.
In this case, should I create the following matrice, here presented for two subjects: (P for patients, T for time point)
P1T1 1 0 1 0
P2T1 0 1 1 0
P1T2 1 0 0 1
P2T2 0 1 0 1
P1T3 1 0 0 0
P2T3 0 1 0 0
Echange block: [1 2 1 2 1 2]
Contrast F test [0 0 1 1] to compare here T1 vs T2?
Also Time point 1 and TP 3 are missing for two different patients. Should I remove these patients for this analysis?
Then to compare patients vs controls, I guess I have to select paired of time points to obtain a 2x2 model.
In this case I obtain this matrix (C for control, P for patients, T for Time point)
C1T1 0 1 1 0 0 0
C1T2 1 0 1 0 0 0
C2T1 0 1 0 1 0 0
C2T2 1 0 0 1 0 0
P1T1 0 0 0 0 1 0
P1T2 1 1 0 0 1 0
P2T1 0 0 0 0 0 1
P2T2 1 1 0 0 0 1
The 1st column correspond to the main effect of time -> F test - Contrast=[1 0 0 0 0 0] - Exchange blocks=[1 1 2 2 3 3 4 4]
The 2nd column correspond to the interaction between group x time -> t-test - Contrast=[0 -1 0 0 0 0] or [0 -1 0 0 0 0] - Exchange blocks=[1 1 2 2 3 3 4 4]
The fourth last columns correspond to the subject means. Should we automatically include it in the design matrix? What does it change?
Sorry for this long email but I'm quite lost! Thanks a lot in advance for your help and insights!
Regards,
Alexia
Threaded View
| Title | Author | Date |
|---|---|---|
| Alexia Bourgeois | Dec 14, 2017 | |
| Leonardo Tozzi | Nov 19, 2019 | |
| Leonardo Tozzi | Nov 18, 2019 | |
| Andrew Zalesky | Nov 18, 2019 | |
| Andrew Zalesky | Dec 16, 2017 | |
| Alexia Bourgeois | Dec 19, 2017 | |
| Andrew Zalesky | Dec 20, 2017 | |