[BioC] quality data check

[Gustavo H. Esteves]

Hello Marcelo,

it seems to me that your data wasn't normalized for dye bias. in general, 
when your data is well normalized, the mean (median) expression values 
remains around zero... I'm not familiar with affy package, but try to look 
at 'normalize' function from this package...

[]s


Gustavo



2005/5/12, Marcelo Luiz de Laia <mlaia at fcav.unesp.br>:
> 
> Dear All,
> 
> We work with cDNA in nylon membranes. We use bioconductor to analyze our
> data, basically, the packages limma, affy and vsn. The normalizations
> are made using normalize.quantiles from affy package.
> 
> However, to verify the quality of the data from this platform is a
> little complicated with the packages bioconductor. We don't know how to
> do, if it is possible.
> 
> Soon, we made one boxplot for each membrane (36 membranes). They are 6
> treatments with 6 biological repetitions. Each gene was printed 2 times
> in the membrane.
> 
> The raw data had been transformed for log into base 2.
> 
> We are with doubt in relation to the interpretation of the graphs.
> 
> [not normalized]
> http://www.lbm.fcav.unesp.br/download/todos.png
> 
> [normalized]
> http://www.lbm.fcav.unesp.br/download/todos.norm.png
> 
> They are:
> 
> 1. it has outliers. The presented amount is very much or is relatively
> normal for this
> platform?
> 
> 2. the box is above of line zero (y axis). That is normal? After
> normalized the data, they are between position 2 and the 3 (y axis).
> This can happen?
> 
> We intend to pick up learn with yours commentaries, therefore, you are
> free to send us any others commentary about the data or quality check on
> this platform. Yours suggestions is very apreciated.
> 
> Thanks very much
> 
> Marcelo
> 
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> Bioconductor at stat.math.ethz.ch
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> 



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Autor desconhecido
_______________________________________________________________


Gustavo Henrique Esteves

e-mail: gesteves at gmail.com
Home Page: http://www.vision.ime.usp.br/~gesteves/

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