Dear Bioconductor Community,
based on the very interesting question on a previous post (batch effect : comBat or blocking in limma ?) regarding the possible batch correction methodologies, through the answers created i desided to adress a very important issue in my opinion-as im still a newbie in these specific statistics-which i also dont have find any relevant explanation in any according paper of MOOC. In detail, Dr Johnson kindly mentioned that limma should not be used in conjuction with ComBat, when the latter applied for batch effect correction. With all respect(and of course without arguing against), i would like to ask some further explanations for this specific matter:
this could be more context and experimental design specific ?? that is, it depends on the magnitude of the batch effect, the variances between the batches, or also the experimental design used in Limma itself(i.e. paired or unpaired comparison) ? Or should someone always avoid it ? And if so, what is the main notion ? (It has to do with the "correlation" mentioned in the above post and possibly with the overestimation of DE ?)
Please excuse me for creating this post, but i believe this question is very important and i would like to get the maximum feedback, because i would like to know (as i used a combination of them in one of my recent analyses) if "still" could the combination considered "valid" under certain circumstances !!
Thank you for your consideration on this matter !!