[BioC] quality data check

[Marcelo Luiz de Laia]

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