Hi, I am given a set of RNASeq fastqs to carry out diff. expression analysis. I have 3 replicates for both control and treatments. I use bcbio for the pipeline that takes care of many steps. Aligner is tophat2. I used DESeq2 for the diff exp part. The results are not very satisfying that in wet lab part the treatment's phenotype is very obvious on proliferation rates yet in deseq2 output the log2fc ranges between 0.5 to -0.4. If I take padj 0.05, there are only 2 significantly enriched genes in total. This does not feel right with such significant phenotype. Has anyone ever come across something like this?