I am performing a differential expression analysis using DESeq2 of a dataset that have a batch effect due to a technical variable.
I am performing the differential expression analysis with two approaches:
- Approach 1: considering the technical variable as covariate in the building of the dds model
- Approach 2: Not considering the technical variable as covariate.
I obtained two lists of genes differentially expressed.
I was wondering if it is correct to compare the two list of genes and consider the more significant genes (TRUE positives) the genes that are identified by both approaches.