I would like to practice differential expression analysis with Tophat/Cufflinks.
I have 6 conditions and each have no replicates.(I understand I should prepare some replicates.)
I executed Tophat mapping and Cufflinks assembly to each condition.
Then, I don't know which of following ways is correct.
・ I should cuffmerge/cuffdiff all 6 condition all at once
・I should cuff merge/cuffdiff each pairwise of 6 samples(namely, 15 times pairwise analysis)
The normalisation in Cuffdiff is for each pairwise? or all conditions?
Anyone has efficient idea fitting my needs.
My English is not good but hope it doesn't cause any toruble.