Dear ALL,

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:

**https://www.dropbox.com/s/k7v8ttbq27pk1xh/prior.plots.COMBAT.png?dl=0**

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 !!!

Dear Evan, thank you for your answer !! Your explanation now makes things clear !! Thus, the up plots you mention for the mean and the down plots for the variance, display the total estimated batch effect for my genes across my two datasets, is that right ?

Finally, as the creator of the methodology, if it is possible--because the above plot it has been produced from some code posted in my previous post--as also some crusial questions posted there:

Appropriate implementation of ComBat function for known batch effect correction and alternative methodologies of merging microarray datasetsYour feedback also would be crusial to certify my whole approach with ComBat !!

Thank you in advance !!

Efstathios