Differential co-expression analysis on TCGA transcriptomic data

Question

[nazaninhoseinkhan]

Dear all,

I am going to use TCGA data with "open" label for my project.

As you probably know, The "open" data are the analyzed data and for example for RNASeq or miRNASeq the normalized read counts (FPKM) have been reported as text files.

Now my question is: if I want to obtain the list of differential expressed genes between tumor and normal samples, what procedures should I use?

Can I use edgeR or Deseq2 on these data which are in txt format?

Thank you in advance

Nazanin