I would like to conduct a microarray meta-analysis of differential expression study of Condition1 vs Condition2 where I could not find many such specific studies with both Condition1 and Condition2 samples. However, there are various experiments that include either condition1 alone or condition2 alone from the same platform.
Could I just download the CEL files for Condition1 and Condition2 from two/three different experiments and process them as usual as a single experiment and identify the DEGs?
(Such an approach was used in https://academic.oup.com/nar/article/45/17/9860/4084660 - see Table 1/SCNvsWB)
However I would like to further make sure that the approach is accurate or Do I need to conduct any batch effect removal algorithms like ComBat before merging the two conditions for a single study?
