[BioC] simpleaffy

Patrícia Luiza Nunes da Costa patriciacosta at lim24.fm.usp.br
Mon Jan 14 21:24:14 CET 2008


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
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.


Patrícia Luiza Nunes da Costa
Laboratório de Oncologia Experimental, Grupo de Adesão Celular
Faculdade de Medicina da Universidade de Paulo-FM USP
Av. Dr. Arnaldo, 455 sala 4112
Cerqueira César, São Paulo-SP
Cep 01246-903
Tel: 55 11 3061-7486 e  55 11 8202-7073

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