Although I understand that removal of batch effects can help with estimating the actual variance in the gene expression data, I would like to know whether the batch corrected gene expression values can be directly used for finding transcriptionally abundant genes across experimental studies?
Thanks for the answer. Very useful for a novice like me. To specify further, I don't want to perform a differential analysis between control and treated samples across studies. I want to take the control of different studies and perform sort of a meta-analysis. In this context, I would like to know whether I can use the batch-corrected average expression of genes to determine a threshold to classify transcriptionally abundant genes.