Hello, I am currently looking at the simpleaffy package for affymetrix data QC. I have a question regarding the 3'/5' ratio reported in the graph and by the function "ratios" This ratio is different from the ratio obtained by using the value reported by the qcProbes() function and making the division "by hand". These 3'/5' ratios are also very different from the one reported with the affymetrix software. Yet, if I use the expression from a call to the mas5() function, the 3'/5' ratio of QC probes is very similar to the one reported by the affy software. I am using the cdf file : "HG-U133_Plus_2" and simpleaffy version 2.0.13 Any help or explanation would be greatly appreciated thanks a lot Paul ----------------------------------------- S - This message contains confidential information and is in...{{dropped}}