11.6 years ago by
Patrícia Luiza Nunes da Costa • 90 wrote:
Friends, I'm beginning the analysis of microarray data from Affymetrix mouse gene chip using Simpleaffy. I did the normalization with RMA and the Quality control was good. I have 4 groups (control, treated1, treated 2, treated 1+2 ) with 3 arrays in each. I was trying to filter the expression values using the parameters: ?significant <- pairwise.filter(results, min.exp=log2(10), min.exp.no=2, fc=log2(2), min.present.no=4, tt= 0.05, present.by.group=FALSE)? According these parameters I had only 6 genes differentially expressed. Isn?t this number very low? I don?t know exactly what means each parameter, nether how I can change any of than (except Fc and tt) according to my experiments. Anybody knows were I can find information about what parameters use for my analysis? I don?t know if I was clear, if not, give me questions please. Thanks, Patr?cia 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 C?sar, S?o Paulo-SP Brazil Cep 01246-903 Tel: 55 11 3061-7486 e 55 11 8202-7073 -------------------------- Esta mensagem foi verificada pelo sistema de antiv?rus DIM e acredita-se estar livre de Virus.
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