Hi everybody! I have been trying to analyze some RNA-seq samples. On one hand I have used Ballgown, with and without adjustvars option, to see the DEG results, as from the PCA plot I can see a strong batch effect between replicates collected on the same days. Then on the other hand, I tryed to use edgeR with TMM method to do the same, with and without adjusting for batch effect. And the thing is that I have really different results. Ballgown always returns a lot of DEGs comparing with edgeR all of them with pval<0.05, but the most surprising thing is that if I compare ballgown and edger results, that there is no common gene name... When I compare edgeR results with and without adujustvar, I have same genes on both results, and some more genes in adjusted option. But with ballgown when I compare edgeR results with an without batcheffect adjust, the results are common in very few of genes.
I know that I haven't write any command, but I have follow pretty well the pipelines described in the protocols and manuals from both sites. So my general question is, are this results typical? I mean, it happens to have different results when comparing different type of normalization, and furthermore, when comparing with and without batch effect adjust?
I'm a little worried about this controversy.
Thanks in advance!