My differentially expressed genes (~600 DEGs) have low fold change (<1). Is this normal and what does it mean?
More details: I work with Zebrafish and had 2 conditions and 12 samples per treatment (24 samples total). I have found around 246-931 differentially expressed genes out of the 23000 or so ensembl annotated genes between my 2 conditions. I say 500-700 because I have tried DeSeq2 (931 DEGs), EdgeR (549 DEGs) and Limma-Voom (246). These genes are FDR controlled at 0.05 and filters like cooks cutoff and independent filtering etc have been applied if applicable. No filtering was applied on fold change. These genes were found to be enriched in 30-40 or so GO terms and 3 KEGG pathways. The GO terms were too vague (cell metabolism, cytoskeletal protein binding etc) to say if they actually mean anything in relation to my treatment. I am a bit concerned about the low fold change. Does this mean that the DEGs are false positives? Or does it mean that the DEGs may be significant and positive but the biological effect is low?