Hi all. 1) I would like to ask for advice on the best algorithm to study genes at the low signal end on Affy chips. I have tried rma gcrma vsn (vsn norm, nbg, medianpolish) liwong mas5 To be honest, although mas5 is very noisy at low end, the real genes (the ones that I know are important and should be there) where clearly out of the noise, where as some of the other methods seem to bury some (but not all) of these genes (in poarticular gcrma seems to bury some genes in the noise at the low end). 2) Reporting fold change The fold change values are dependant on the analysis algorithm, in mas5 the fold changes are very high at low end, but not in rma. Is this real (ie I would expect in any assay that the low end signal is more noisy and variable at low end, therefore low end genes would have to have large fold change to stand out of noise on M vs A plot) Any advice gratefully recieved Anthony -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au