I am dealing with RNA Seq data, where I am studying if the expression of a set of genes is subtype specific. For this, I have plotted the expression of the genes across the different subtypes, but to make sure if the data is significant, I wish to perform a t-test on the samples where I see a difference between any two molecular subtypes.
I performed the t-test with the
t.test() function in R and I have two questions regarding the output -
First, at times it gives me an accurate p-value, for example, 3.921e-14, but at times it just says p-value< 2.2e-16. Is that the minimum p-value displayed, or can I get an accurate p-value?
Secondly, the confidence interval by default is 0.95, which I changed to 0.99, 0.999 and so on. Yet, I never seem to find any difference in the p-value. To confirm there is no change, I also tried confidence intervals of 0.5 and 0.1.
Any help or advice on the two points would be greatly appreciated.