I have a few genes, where rtPCR has been done. I have normalized the arrays with mas5, rma and gcrma. Here are the Fold Changes of the genes. GCRMA shows the biggest correlation with pcr. Still I cannot figure out any systematics except that gcrma shows smaller values. If a cut off fold change of 1.5 is taken, only 3 genes are being selected. The distributions of the normalized signals look very different. GCRMA shows a bimodal distribution. Furthermore, does anybody know if there exists smth like a change p value for rma or gcrma, like in the mas5 software? Thanks a lot for your help mas5 pcr rma gcrma BTG2 -1,5 -1,5 -1,6 -1,3 EFNB2 -1,6 -1,4 -1,6 -1,4 EPAS1 -1,8 -1,4 -3,1 -1,6 EZH1 -2,8 -1,5 -1,2 -1,1 FN1 -1,9 -1,4 -2 -1,7 FOXF2 -1,5 -1,4 -1,1 -1,1 MMP14 -1,9 -2,0 -2 -1,6 PTBP1 -2,2 -1,3 -1,9 -1,4 VIL2 -1,4 -1,6 -1,5 -1,3