[BioC] minimum expression level (Simpleaffy)

Mon Jan 28 16:34:14 CET 2008

Hi Patricia,
Between 2.15 - 14.6 sounds about right. Remember the intensities are in log scale after GCRMA or RMA.

In my last affymetrix analysis I think I used ~ 3.5. It was decided in an ad-hoc way by looking at the distributions: those under this threshold in my dataset also had very low variability across samples. 10 seems very stringent cut-off to me. Making plots of your data can help you decide what threshold to use.

Best wishes,
Alex

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Roslin Institute (Edinburgh)
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-----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: 28 January 2008 13:12
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] minimum expression level (Simpleaffy)

Hi group!

After normalization of expression data, using SimpleAffy, we observed low fluorescence intensities to every probesets, between 2,15 and 14,6 (mean= 5,78).
What value should I set to minimum expression level?
For Affymetrix experiments, the default here has been set at log2(10), but I think it seems very stringent to my data, what do you think?

Thanks and regards,
Patrícia

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 Cesar Cep 01246-903
Tel: (11) 3061-7486 e (11) 8202-7073

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