Is it possible to perform trend test for case control genetic association in spss.
I performed ANOVA to test any difference between the three genotype groups, and found significant differences. However, the reviewer asked for additive model trend test as follows:
"Most genetic analyses are performed on a additive scale (trend). All p-values and estimation done in this manuscript are based on ANOVA (is there any difference). I would like to see what happens when you perform all test on an additive scale. p trend with linear regression. I expect not different results for the SCAP gene, however it might be that the SREBF-1a association disappears".
How to perform and interpret this on SPSS?
Thanks and regards
Cochran-Armitage (CA) test is not available in SPSS, but for trend test ,you can use Linear-by-Linear Association (LLA) test instead if you only use SPSS.
Here is what said by help document in SPSS:
SPSS does not provide the Cochran-Armitage (CA) test directly, and a request has been filed with SPSS Development to add this statistic to Crosstabs output where applicable. However, the test statistic can be derived from the Linear-by-Linear Association (LLA) test for trend results of the Crosstab procedure, provided that either the row or column variable is dichotomous. The LLA test for trend equals (N-1)*r^2, where N is the sample size and r is the Pearson correlation between the 2 variables. (See Technote 1477269 for more information on the LLA test, also known as the Mantel-Haenzsel test for trend. This test is not related to the Cochran-Mantel-Haenzsel tests for common odds ratio that are also available in the Crosstabs procedure.) The null hypothesis for each of the LLA test and the CA test is that the linear trend parameter is 0, so a significant p-value for the test is consistent with the presence of a trend.
In spss case, I use Jonckheere-Terpstra test when I'd like to test trend test.
Thank you Dr Matuka...even Kendal-Tau would also give the same results, but genetic epidemiology people like CA trend test ..
SPSS does not provide the Cochran-Armitage (CA) test directly...so you use expand development.
Really an amazing explanation. Thank you very much Adela Jing Li. Linear contrast analysis is something new for me. Thank you very much once again!!
Cochran-Armitage (CA) test is not available in SPSS, but for trend test ,you can use Linear-by-Linear Association (LLA) test instead if you only use SPSS.
Here is what said by help document in SPSS:
SPSS does not provide the Cochran-Armitage (CA) test directly, and a request has been filed with SPSS Development to add this statistic to Crosstabs output where applicable. However, the test statistic can be derived from the Linear-by-Linear Association (LLA) test for trend results of the Crosstab procedure, provided that either the row or column variable is dichotomous. The LLA test for trend equals (N-1)*r^2, where N is the sample size and r is the Pearson correlation between the 2 variables. (See Technote 1477269 for more information on the LLA test, also known as the Mantel-Haenzsel test for trend. This test is not related to the Cochran-Mantel-Haenzsel tests for common odds ratio that are also available in the Crosstabs procedure.) The null hypothesis for each of the LLA test and the CA test is that the linear trend parameter is 0, so a significant p-value for the test is consistent with the presence of a trend.
hello sir Misbahuddin rafeeq how could you perform Cochran-Armitage (CA) trend test using spss?
can we perform it on 2*2 as well as 2*3 contingency table?
I am also doing case control study and have to select one best fit genetic inheritance model for my study.
I am facing the same problem in my gene study i know how to calculate the CA test from linear by linear association on spss However, i couldnt understand how to get its p value and OR Hong-Qiu Gu
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