I don't have access to the raw files. I have access to the
htseq-count FPKM FPKM-UQ
I have read all the questions asked in here. However, I still cannot find a good solution to the following questions
1- I want to find up and down-regulated genes, which package normally do you use and how do you convert them to the gene names?
2- which one of the above files are more reliable ? do you have any publication to refer to?
3- They come from TCGA, however, I cannot get the raw RNA seq and that is why I am trying to do the analysis based on one of the above files.