[BioC] simpleaffy

Celine Carret ckc at sanger.ac.uk
Tue Jan 15 12:06:44 CET 2008

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

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Patrícia Luiza Nunes da Costa
Sent: 14 January 2008 20:24
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] simpleaffy


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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