Hi, I analysed RNA seq data recently using UCSC knowngene as annotation file and found several differentially expressed genes. Then I confirm DEGs (P-adj<= 0.05) by real-time PCR and found consistency between rna-seq data and real-time PCR data. But when I analysed same data using same analysis pipeline but with GENCODE annotation files, I found that genes those were down with UCSC knowngene annotation are still down (except for some) but the p-adj is > 0.05 (for one of the gene it is 0.22). I want to understand why there is discrepancy between two analyses and which p-adj values shall I consider?
Any suggestion would be appreciated.