Hi, I am going to do affy analysis for the first time. After reading the previous related postings, I have some questions: 1. If I use the RMA method to estimate the true intensities, should I neglect the present call/absent calls? 2. If I should neglect the present/absent calls, is there any other another equivalent variable that is similar to the weights or flagged poor values in 2-channel data? 3. If I should still use present/absent calls, are they included in the latest affy package? How should I use the calls with the results generated from RMA method? 4. Any pointers, especially using affycomp, for choosing a good combination of background correction, pmcorrection, normalization & summarization methods? Thanks in advance! Regards, Fai ________ Yuk Fai Leung Bauer Center for Genomics Research Harvard University 7 Divinity Avenue Cambridge, MA 02138 Tel: 617-496-7134 Fax: 617-495-2196 email: <mailto:yfleung@cgr.harvard.edu> yfleung@cgr.harvard.edu; <mailto:yfleung@genomicshome.com> yfleung@genomicshome.com URL: <http: genomicshome.com=""> http://genomicshome.com [[alternative HTML version deleted]]