Hi Fabio,

As for the internal quality control of Illumina microarray, we have added
some functions in the lumi package (developing version). These functions
deal with the control probe information. Please check the help information
of addControlData2lumi, plotControlData, plotHousekeepingGene and related
functions. Currently, the quality control is mainly based on the
visualization. You can read the Illumina BeadStudio manual to get some ideas
of the interpretations. We will further improve this part later on.

As for the VST algorithm, the related paper has been published in Nucleic
Acid Research, please cite it if you use it:

http://nar.oxfordjournals.org/cgi/content/abstract/gkm1075v1?ck=nck


Thanks for using lumi package,

Pan Du


On 2/1/08 2:49 AM, "fabio manzo" <fabiomanzo25@gmail.com> wrote:

> Dear Dr. Pan Du,
> How you know I'm using your lumi package, that 's, as beginner, I found  it
> really user friendly. I was reading the various Bioc discussion about the
> quality control and it seems that's still not available with the lumi package.
> Is it true? If it's, may i ask you what can I do? What other resources I can
> use and how I can evaluate if my data are all right. I applied a vsn
> normilization on the raw data, avoiding the vst transformation. The histogram
> obtained looks all right. But for controlling internally the data what can i
> do? I hope of not disturbing you too much, but I  didn't understand how to do
> this part with the illumina array. Thanks a lot,
> Best,
> Fabio
> 
> P.S.
> in the raw data after bead studio:
>   
>  Illumina Inc. BeadStudio version 1.5.0.34 <http://1.5.0.34>
>  Normalization = none
>  
>   
>  Array Content = Human_RefSeq-8.xml
>  Error Model = none
>  
>   
>  DateTime = 25.08.06 12:14
>   
>  Local Settings = en-GB
>  


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