Hi, I managed to remove the batch effect I mentioned here: A: Batch effect correction using ComBat function (sva package). PCA plot seems ok:

Now, when I look at MA plot of samples from the same plate I get this weird result:

while the MA plot pre-removal of batch effect looks like this:

Can someone please enlighten me why it looks this way? what exactly ComBat is doing to my data? How can I deal with this? Thanks!