My PI would like to know if three key proteins are expressed in patients with a particular type of cancer. I can find some online sites, such as Firehose and OncoDB, that could graph this for me, but I want a little more control over the graphs and I also want to know HOW they're quantifying the expression
That said, what would be the best way for me to do this/what is the most widely accepted way of finding protein expression in TCGA datasets?
From what I gathered, the only way to kind of answer this is by looking at the RNA seq data, and TPM is the best way to normalize RNA seq data. I AM able to get the raw counts from the GDC. However, how should I go about converting these counts to TPM? Is there a tutorial?
alternatively, if there a different method I should be using?
