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Old 01-16-2014, 10:15 AM   #2
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Location: UK

Join Date: Jan 2010
Posts: 390

In all honesty I would advise you not to proceed until you have clarified the goals of your experiment. You are not in a position where you can draw meaningful information about your samples other than quantifying the transcripts in them, if this is of interest to you, then go ahead. But there's no route for differential expression. Using blood as a control is of no use to you, all you're going to tell is what is different between blood and brain tumour - hardly the biological question you're going to want to ask.

I suppose you could try and find some 'normal' pituitary RNA-Seq data from somewhere else and use that as a control but I can tell you now that the individual variation between your samples (with so few samples) is likely not going to provide you with anything meaningful.

Why don't you tell us why you are doing this experiment and what you hope to find out from it? That might help more.
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