I'm now trying to follow the "HISAT2+StringTie+Ballgown" pipline in Nature protocols to do RNA-seq Analysis. In Ballgown analysis, the author of the protocols used a "pheno_data.csv" to give the group information. I'm confused about that. My data is:
ids groups reps ERR1 CCI rep1 ERR2 CCI rep2 ERR3 CCI rep3 ERR4 Sham rep1 ERR5 Sham rep2 ERR6 Sham rep3
What is confusing me is that in their protocols, they had three column (ids, sex, population), So in
stattest they set
covariate="sex", adjustvars=c("population") and I set
covariate="groups", adjustvars=c("reps"). However, there is no DE genes in the final results (all qval > 0.05). So I guess there maybe something wrong with my pheno_data. Could someone help me about this?
I'll be very appreciated if you can help me!