in conjuction with one previous post about the correct implementation of ComBat() function for batch effect correction, [Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasets]
i would like to ask for the interpretation of the resulting plot regarding the parametric approach, and how could i investigate it for my results. The link to the plot is below:
So, i understand that the black line represents the kernel estimate of the empirical batch effect density, and the red the parametric estimate, but why there are two lines of plot ? In other words each line of two plots what represents ?
Moreover, regarding the evaluation of the plot, mostly on the density plots, i could consider the parametric adjustment efficient or not ?
Finally, before implementing Combat, a standardization of my merged microarray dataset, could be considered beneficial for the parametric approach ?
Please excuse me for any naive questions, but i have no experience with previous diagnostic plots regarding ComBat, and any feedback is highly appreciated !!!