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.

Hello Patricia, You certainly can have a look at ?pairwise.filter in your R session to see what options are available for this function. That will show what each parameter means. Thus you'll see that the criteria you chose are very stringeant! You certainly can relax the stringency on the fc for exemple, or relax the stringency on the minimum expression you want to see. I hope this helps Celine -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Patr?cia Luiza Nunes da Costa Sent: 14 January 2008 20:24 To: bioconductor at stat.math.ethz.ch Subject: [BioC] simpleaffy 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. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.