Hi,

I intend to integrate two microarray datasets with imbalanced outcome. First of all which method has shown the most robust results in this context. My current options are ComBat and RUV-2.

Second, I searched on how to use ComBat. I found this article highlighting the fact that taking into account the study outcome as a covariate will exaggerate the confidence of downstream analysis. On the other hand there is this post by the package author which suggests using the outcome as a covariate in addition to the batches. Now I am not sure which one to choose.

Thanks in advance!