[BioC] info su illumina

[Giovanni Coppola]

Hello Lynn,
I am trying to analyze Illumina (Sentrix BeadChip Mouse Ref8) data  
with the beadarray package.
All I have is:

1) a geneprofile.csv (matrix with expression values)
2) for each array strip, three files (.idat, .jpg, .xml)
3) one .sdf file
4) metrix.txt
5) the illumina CD with beadmap files
6) one copy of the BeadStudio software

I assume I can't use the beadarray package, is that correct?
Can I use the BeadStudio software to obtain bead level text files?
Thanks
Giovanni

On Feb 8, 2006, at 10:18 AM, Lynn Amon wrote:

> One possibly helpful note about Illumina arrays is that you need to  
> make
> a change to the Settings.xml file in the ProgramFiles/Illumina/ 
> BeadScan
> directory in order to get summary or bead-level text files which can
> then be read in using read.table or with the beadarray package.
>
> Change the line:  <SaveTextFiles>false</SaveTextFiles> to
> <SaveTextFiles>true</SaveTextFiles>
> and add the following line if you want bead-level data:
> <SavePerBeadFiles>true</SavePerBeadFiles>
>
> Keep in mind that the bead-level files are large especially for the
> whole genome chips.
>
> Lynn Amon
> Research Scientist
> Department of Pathology
> University of Washington
>
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