Intersecting Wald DESeq2 Results
I am analyzing differential expression among three different factor levels (control samples, samples with overexpression (OE) of gene of interest, and samples with knockout (KD) of gene of interest). I understand I can use the likelihood ratio test to look for general expression changes among the three conditions at once. However, could I also intersect pair-wise Wald test results for control vs OE and control vs KD? E.g., genes that are both significantly downregulated in knockout samples and upregulated in overexpressing samples (compared to control samples).
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