open-discussion
open-discussion > RE: Performing Correlation test
May 27, 2015 09:05 AM | D J
RE: Performing Correlation test
Hi Clement,
I've been wondering about the same issues. I've come to some conclusions, but would certainly appreciate conformation from Martin or Beatriz.
Initially, I believe your command line is missing an argument specifying your input columns, something like: –columnIndependent 2,3,4 (with 2 being your clinical score and 3 and 4 being your covariates).
1. While it looks like this should work, the correlation test (Pearson & Spearman) does NOT consider the covariates, just runs against the --testColumn. It even says so much in the output, that the result is uncorrected, or something similar. You can confirm this by running the analysis with and without the covariates and the Pearson/Spearman output will be identical. Additionally, in the source code there is consideration for correlation with covariates but it not implemented.
2. From my understanding, the MANOVA test is valid and DOES consider covariates, and so can provide p-value/FDR p-value maps. However, the MANOVA test cannot provide a single coefficient to provide the direction of the change (like the Pearson R). Both these points can be demonstrated in SPSS by running a MANOVA with some covariates – a group test/factor is not necessary. Obtaining a direction is possible using correlation testing though, because only one dimension is used (inflation/deflation along the difference vector or the normal) and so can provide a single description of inflation/deflation. This also explains why the MANOVA significance maps and correlation significance maps are slightly different – the first is using a MANOVA on 3D coordinates, whilst the second is using vectors collapsed from the 3D coordinates.
In summary, MANOVA shows covariate-corrected significance tests, but doesn't tell you the direction, and Pearson/Spearman can tell you direction and significance, but not using covariates.
This is my working assumption – very happy to be corrected by the SPHARM team though!
Hope this helps,
Dave.
I've been wondering about the same issues. I've come to some conclusions, but would certainly appreciate conformation from Martin or Beatriz.
Initially, I believe your command line is missing an argument specifying your input columns, something like: –columnIndependent 2,3,4 (with 2 being your clinical score and 3 and 4 being your covariates).
1. While it looks like this should work, the correlation test (Pearson & Spearman) does NOT consider the covariates, just runs against the --testColumn. It even says so much in the output, that the result is uncorrected, or something similar. You can confirm this by running the analysis with and without the covariates and the Pearson/Spearman output will be identical. Additionally, in the source code there is consideration for correlation with covariates but it not implemented.
2. From my understanding, the MANOVA test is valid and DOES consider covariates, and so can provide p-value/FDR p-value maps. However, the MANOVA test cannot provide a single coefficient to provide the direction of the change (like the Pearson R). Both these points can be demonstrated in SPSS by running a MANOVA with some covariates – a group test/factor is not necessary. Obtaining a direction is possible using correlation testing though, because only one dimension is used (inflation/deflation along the difference vector or the normal) and so can provide a single description of inflation/deflation. This also explains why the MANOVA significance maps and correlation significance maps are slightly different – the first is using a MANOVA on 3D coordinates, whilst the second is using vectors collapsed from the 3D coordinates.
In summary, MANOVA shows covariate-corrected significance tests, but doesn't tell you the direction, and Pearson/Spearman can tell you direction and significance, but not using covariates.
This is my working assumption – very happy to be corrected by the SPHARM team though!
Hope this helps,
Dave.
Threaded View
Title | Author | Date |
---|---|---|
Clément Bournonville | May 27, 2015 | |
Clément Bournonville | May 29, 2015 | |
D J | May 27, 2015 | |
Clément Bournonville | May 27, 2015 | |
D J | May 27, 2015 | |
Beatriz Paniagua | May 27, 2015 | |