dpryan, that's good advice. I want to input my results into SPIA, and a couple of pretty cool pathways pop up, but some of thse are fold changes of 1.3 or so (very highly expressed, which is why DESeq called it). I doubt I could get it to pop up on qPCR. Would you say its fair to then say that RNA-Seq has better resolution than qPCR?
ThePresident, if you have fold changes over 2, you should do qPCR. You should be able to show fold changes and it strengthens your case. What I would say is that you do qPCR on your RNA samples, and assuming you have replicates, do qPCR on the replicates as well. Have it in triplicate, that way you are now doing technical noise (RNA-Seq vs. qPCR) and you are doing biological noise (from doing 3 replicates).
ThePresident, if you have fold changes over 2, you should do qPCR. You should be able to show fold changes and it strengthens your case. What I would say is that you do qPCR on your RNA samples, and assuming you have replicates, do qPCR on the replicates as well. Have it in triplicate, that way you are now doing technical noise (RNA-Seq vs. qPCR) and you are doing biological noise (from doing 3 replicates).
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