Dear colleagues, We are trying to analyze a group of Affymetrix arrays, but we don?t have experience. We performed the RMA normalization and after we analyzed with the algorithm SOM (3x3 Expander), among others. We observed that some control genes was differentially expressed in 2/12 arrays (Cluster are attached), and it shoudn't, isn't it? The QC stats plot (simpleaffy) seemed good (attached), and all parameters indicated by Affymetrix showed results acceptable. Do you think we have a bug in the experiment? Should we compare this 2 ?different? arrays with the others? Or can we correct this? Thanks for your help! Patricia Patr?cia Luiza Nunes da Costa Laborat?rio de Oncologia Experimental, Grupo de Ades?o Celular Faculdade de Medicina da Universidade de Paulo-FM USP Av. Dr. Arnaldo, 455 sala 4112 Cerqueira Cesar Cep 01246-903 Tel: (11) 3061-7486 e (11) 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus.