[BioC] mas5, gcrma, rma

[Auer Michael]

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