Dear expert,
I have runed cufflinks 1.0.3 to get the FPKM value for each Illumnina RNA-seq pair-end sample.
When run cufflinks, I do not set these parameters:
--upper-quartile-norm
--total-hits-norm
--compatible-hits-norm
Now I want to do normalization between samples, does anyone have some suggestions? Using DEseq? or Limma?
Thank you very much in advance.
I have runed cufflinks 1.0.3 to get the FPKM value for each Illumnina RNA-seq pair-end sample.
When run cufflinks, I do not set these parameters:
--upper-quartile-norm
--total-hits-norm
--compatible-hits-norm
Now I want to do normalization between samples, does anyone have some suggestions? Using DEseq? or Limma?
Thank you very much in advance.