Hello,
I am analyzing TCGA data, RNA SEQ, of tumoral tissues. I would like to perform a correlation analysis with gene expression (to see if gene expression of Gene 1 correlates with Gene 2 in the sample, for example) and some clinical data (like alpha-fetoprotein levels, age, bilirubin levels...).
My doubt is: should I use FPKM data or normalized counts generated by Deseq2? Or something else?
Thank you!
Ok thanks! But my main concern is what type of data should I use for input for analysis in this case.
Input to DESeq2 and SAMseq is original counts, not scaled counts ("normalized counts"), and not FPKM.