This study demonstrates a successful application of alternative analysis methods to detect differentially expressed genes in a genome wide expression study when standard methods fail. SYBR Green RT - Real time PCR proved as a reliable method to confirm the results of the array analysis. Four genes with different expression levels in at least two muscles (SQSTM1, SSRP1, DDIT4, and MAF) are assigned to transcriptional cascades related to cell death and may thus indicate pathways for further investigations on congenital splay leg in piglets.