I am looking at affymetrix microarray data from normal and cancer cells that I found on GEO. I want do stats on the expression level of just one gene of interest between normal and cancer cells. I have done some reading and I am just looking for confirmation that my approach is correct.
I am starting from CEL files (which I hopefully understand are just the raw intensity measurements for each probe).
I read these CEL files into R and know how to get a dataframe like object where each column is a different sample, each row is a probe, and each data entry is a raw intensity value
The way I understand it, next I would probably do RMA normalization which would normalize these raw intensities between samples and would output log2-transformed and normalized intensities.
I know that if I now wanted to find all DE genes I would go to something like limma at this point and use proper methods to control FDR, but my main question is if I wanted to just look at a single probe or two can I just do a simple t-test on the RMA normalized intensities?
Thank you for your time.