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Hi,
I have a relatively simple RNA-Seq experiment. I have 10 samples in my control group and 10 samples in my treatment group. Each sample is from a different patient. How can I test for differences between control and treatment groups but control for the natural differences we might see between patients. Your help is greatly appreciated.
Thank you for the response. So I do not see any differential expression when using design =~ condition and p-adj < 0.1. Is there anything else I can modify or try? Also, if I look at p values instead of p-adj then I see some differential expression (about 1000 genes).
Unadjusted p-values are not the right thing to be looking at. Stick with adjusted p-values. As always, XKCD explains why: https://xkcd.com/882/
Take a look at the MA plot (see vignette). This will give you a senses of the differences across treatment. You can also look at the plotCounts() function to see why the top gene doesn't have an adjusted p-value less than 0.1. This typically means small differences across group relative to the variance within group.