New to TCGA. I want to compare something in between all liver hcc samples from different patients and was wondering if the raw count output from unstranded can have tmm done on it so I can filter out samples with a low count for a particular gene I am investigating. Or can I simply use FPKM or TPM to just do this filtering out. From what I have read online I see that it may not be a good idea to use TPM or FPKM to compare between samples. Even though these are all primary liver hcc tumors there may still be big differences in libraries and preparation. Does using tmm normalization on the raw counts provided from all of these samples coalesced together enable me to then compare between the samples and filter out tumor samples by the tmm counts for a particular gene as a means of comparison before doing differential expression analysis? I would like to have two groups and compare. One group with high expression of this gene and the other without/low to see differences present when this gene is present.
