I have RNA seq data from two different experiments, but both experiments are related to one factor (alcohol effect). The first one has been done on tissue and the second experiment has been done on cells. I am interested to find a group of genes related to the alcohol effect vs the control groups. Any suggestion or idea about which analyses I should use.
Have thought about using a differential expression analysis?
Using a program such as DESeq2/edgeR/Limma to compare your tissues with or without treatment ( ~ alcohol_treatment) and your cells with or without treatment ( ~ alcohol_treatment) separately. Then looking in those two analysis which genes are statistically significant in your two experiments and take them as best candidates?