Hello everyone, I have been working on expression analysis past few months. Lately, I hadn't been asked to address batch effects from my data. I have two datasets on which I had performed a meta-analysis. I had certain questions regarding batch effects and removal of batch effects removal from my data.
Q - 1. I had read that the batch effect removal algorithm is required when your approach is "Data Merging" and not "Meta-analysis". I hadn't merged my data - Just performed limma analysis and then check for common genes and finally used the pval combination method. Finally, find out DEGS. I hadn't found papers that address batch effect removal in such a strategy. Please help.
Q. 2 - Secondly if I performed sva on the individual dataset, perform limma analysis and then use the pVal combination method to combine the dataset. Is it possible?
Q -3.How to create a model and null matrix and finally how to get the batch effect adjusted expression matrix.
Kindly help. Thanks in Advance.