[BioC] minimum expression level (Simpleaffy)

[alex lam (RI)]

Hi Patricia,

The exprs() function will return a matrix of expression values, with rows being probesets, and columns being samples. For example you can get the mean expression value for each probeset like this: apply(exprs(your.eset.object), 1, mean)

This will give you one value per probeset.

Then, for example, you can plot a histogram using hist() to inspect the expression distribution.

Apart from mean, you can also look at statistics like median or max to decide what is the cut off for low signal.

Good luck,
Alex

-----Original Message-----
From: Patrícia Luiza Nunes da Costa [mailto:patriciacosta at lim24.fm.usp.br] 
Sent: 28 January 2008 16:18
To: alex lam (RI)
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] minimum expression level (Simpleaffy)

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



--------------------------
Esta mensagem foi verificada
pelo sistema de antivírus DIM e
acredita-se estar livre de Virus.