Entering edit mode
5 months ago
Javier
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0
I was wondering if I can perform an Enrichment Analysis from results obtained by RT-qPCR. I know you tipically do this with some sequenced results, but I have 50 genes done by RT-qPCR
Thanks in advance
Since these genes will not be randomly chosen, you must know why you tested them. With 50 genes I see no point running enrichments. Just look at the data and apply biological knowledge. Or intersect them with REACTOME or KEGG terms to learn what they're involved in, but don't calculate any stats (like a pvalue), which is meaningless with that few genes.
Yes, I do know where the genes come from and of course I link the genes to biological knowledge or background of my hypothesis, but still, I think looking for which pathways they belong beyond the most known attributes of these genes Appreciate your answer
Yes, then really just intersect annotated pathways with these genes and see what makes biological sense. You don't need statistical significances for this. If I see something like IL-1ß and CASP1 in my gene list then I don't care about any pvalues, then I check and validate that there is inflammation and apoptosis going on. Probably something similar is true for your case.
You posted this on multiple forums at the same time, which is bad etiquette. Please don't do this in the future unless you wish to annoy users in all communities involved.
Cross-post link: https://bioinformatics.stackexchange.com/questions/21922/feasibility-of-enrichment-analysis-from-rt-qpcr-results
Didn't know it was a bad practice to ask for help in different platforms. Never intended to annoy
I apologize - I was too harsh with that comment. It's not a good practice is all. It's like saying "both" when someone asks you if you'd like tea or coffee.