Hi, I ve been trying the new FARMS library to analyse primary signals of Affy U133A chips (using R2.4dev downloaded yesterday on a PC with winXPPro) which according to a recent publication in Bioinformatics is more accurate than RMA / gcRMA etc... Why is it that I get for more than 3/4 of the probesets the same signal values for all chips for a given probesets ? and this in multiple different set of chips. Such as probeset1 gave for chip1, 2, 3, etc... the same intensity values for all chips ??? Is it because of the normalisation process proposed here ? I m septic... BTW, I used the q.farms function there in such a way: data1 <- ReadAffy() data2 <- q.farms(data1) thank for the help regards Philippe Guardiola, MD