Comparison DESeq results using different model

Question

[concetta]

Hi!

I am performing a differential expression analysis of a dataset that have a batch effects due to a technical variable.

I am performing the differential expression analysis with two approaches:

1. Approach 1: considering the technical variable as covariate in the building of the dds model
2. 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.

Thank you,

Concetta