RNA seq data analyses

Question

[saj98]

Hello everyone

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.

Thanks for help Shaima

[saj98]

I used cummeRbund to look for genes expression and sig genes. I am interested to do cross-species analyses to get the significant genes are related to alcohol effect.

Answer 1

[VHahaut]

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?