[BioC] minimum expression level (Simpleaffy)

Patrícia Luiza Nunes da Costa patriciacosta at lim24.fm.usp.br
Mon Jan 28 17:18:10 CET 2008


Hi Alex!

Thanks for your suggestions!
I think I understood. But, I don’t know how to make these plots (I’m a new
user of  “R”). Do you have any manual or exercise that could help me?
I’ve tried to make its using simpleaffy commands, but it doesn’t work. I
had the error below:
plot(significant, type="scatter")
Error in .local(x, y, ...) : unused argument(s) (type = "scatter")

Thanks again!!!

Patricia



> 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
>
> --------------------------------------------
> Alex C. Lam
> Roslin Institute (Edinburgh)
> Midlothian
> EH25 9PS
> United Kingdom
> Tel: +44 131 5274471
>
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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
>
>
>
>
> 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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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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