Hello,
I'm wondering if you might be able to share any thoughts on the behavior of QQ plots from the p-values of a treeWAS analysis. In my data, I am seeing a pattern of "inflation" (consistent deviation of observed values above the y=x line - plot attached), which is apparently consistent with population stratification. I know that generally treeWAS aims to "control for the confounding effects of clonal population structure and population stratification", but it's not clear to me how this may or may not alter the observed p-values produced by the treeWAS tests. If my samples are somehow stratified (which seems quite likely for almost any bacterium), should I expect such a pattern of "inflation", even with the controls applied by treeWAS? Is the observation of such a pattern problematic, and, if so, are there alternative approaches (within or beyond treeWAS) that I might try?
Hello, I'm wondering if you might be able to share any thoughts on the behavior of QQ plots from the p-values of a treeWAS analysis. In my data, I am seeing a pattern of "inflation" (consistent deviation of observed values above the y=x line - plot attached), which is apparently consistent with population stratification. I know that generally treeWAS aims to "control for the confounding effects of clonal population structure and population stratification", but it's not clear to me how this may or may not alter the observed p-values produced by the treeWAS tests. If my samples are somehow stratified (which seems quite likely for almost any bacterium), should I expect such a pattern of "inflation", even with the controls applied by treeWAS? Is the observation of such a pattern problematic, and, if so, are there alternative approaches (within or beyond treeWAS) that I might try?
Thanks!
qqPlot.pdf