Hi bioC community,
Until now I used comBat to remove the batch effects present on my datasets.
After reading the article "Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses" http://biostatistics.oxfordjournals.org/content/early/2015/08/31/biostatistics.kxv027.full.pdf, I decided to block for batch effect in limma in the case where the groups are distributed between the batches in an unbalanced manner.
But I am wondering what is recommended when the groups are balanced between the batches : use combat and then limma without taking into account the batch effect or introduce the batch variable in an additive manner (blocking) in the limma analysis ? Which approach is the more powerful ? Do you have recommendations to give ?
Thanks in advance for your help,