Apologies for a, probably very simple, question but I am stuck on something. We performed whole RNAseq analysis on large intestinal tissue and performed a differential expression analysis using EdgeR. I now want to perform IPA core analysis on the differentially expressed genes (FDR<0.05). I have watched the IPA tutorial and it looks straightforward enough, the thing I am wondering about if I need to feed in the logFC values generated by EdgeR or that I need to convert them to fold change values and then add them into IPA? Also, should I run the analysis only against Large intestinal tissue or against all cell types? Quite a few samples get filtered out when I solely select large intestinal tissue...
You don't "need" the log fold change values, however, they add statistical power to your IPA analysis (i.e. make your results more accurate). You do not need to convert the log fold changes generated with EdgeR. I would run core analysis with only large intestine, and then try it with other cell types. See how the results differ (i.e. you might have different immune cell types within the blood of the large intestine tissue samples you compared.)
You can run IPA with gene lists for your species of concern for which the transcriptome is done. Usually it tries to find enrichment of pathways based on your genes of interest against their knowledge base which mostly is from experimental ecidences. You should be using core tox analysis. You can see the representation for different cell types and for specific cell types. However logFC values can be supplied as an additional column which might help you to visualise if your genes having both up and down DEGs if significant for any pathways , which DEGs are driving the pathways. It is always informative to see pathways enriched with total DEGs with logFC values to see impact of up and down genes in a pathway significantly enriched or just run up or down gene list separately to see significant pathway enriched. The logFC will give the directionality which guides the genes that dictate the pathway.
I don't think developers of IPA are active on this website. Since it is a commercial package/company, you can ask support directly to them.
Good luck!
I will do that, I just assumed it was a problem a lot of people ran into.
Thank you for your advice!