I am working through the Reference based RNA-SEQ data analysis tutorial and am at the stage where the differentially expressed genes are being run through goseq. However, I see that in the previous step (compute), we only add one expression to select for significant adjP.values (bool(float(c7)<0.05)). Don’t we also need an expression to determine the significant log2FC? And how would we add this in the expression statement? Many thanks for the clarification!
See this part of the tutorial Reference-based RNA-Seq data analysis for FC manipulations.
The End-to-End Analysis trio of tutorials will also have more content about pathways/GO.
And, of course, you don’t have to do exactly or only what is in the tutorials. Those are just examples to get you started and exploring on your own more ways to slice the data is encouraged and expected. Maybe you’ll come up with a novel method, or adapt some other known method (from a publication, or mentioned at some general biology forum).
What code should we include to determine the significant log2FC? (bool(float(c7)<0.05)) only determine adj.p?