[BioC] info su illumina

[Mark Dunning]

Hi Giovanni,

You will be able to analyse this data using 'beadarray'. The package is able
to read bead-summary data which has been processed by BeadStudio (a single
averaged value for each bead type on an array) or the bead-level data. If
you make the modifications that Lynn suggests you will able to extract
intensities of each bead using the scanning software. It does not sound like
you have these files though. However, to make full use of the beadarray
package you would also require files which give the coordinates of each bead
on each array. Unfortunately, Illumina seem quite reluctant to give out the
bead centre coordinates at the present time. We are however pressing them to
make this information available.

I think the best way for you to proceed would be to read the file
geneprofile.csv into beadarray. The quickest way to do this is to put the
file in a directory on it's own, change the R working directory to point to
this and use the "readBeadSummaryData" command from beadarray. You will
probably need to use the columns parameter to specify the names of the
columns that are being used in the file. I believe the following command
will work for the standard output from BeadStudio

BSData = readBeadSummaryData(columns=list(ProbeID="TargetID",
AvgSig="AVG_Signal", Nobeads="Avg_NBEADS", BeadStDev="BEAD_STDEV", Detection
="Detection"))

This will then create a list object similar to the RGList object used in
'limma', ie the expression values are in the $R matrix with rows
representing genes and columns representing arrays. This expression matrix
can be used for clustering, pca, linear modelling (via limma) or
normalisation. So far we provide median, quantile or qspline normalisation -
although methods within the 'affy' package could also be used. Additionally,
the 'plotMAXY' function will give scatter and MA plots for multiple arrays
and is a useful way of judging array quality.

btw do you know how the data in geneprofile.csv was normalised by
BeadStudio? Illumina recommend a rank invariant normalisation plus
background correction, but that seems like a very bad idea to me looking at
some of the data it produces!

Please let me know if you have any further questions or comments. The
package is still in the development stage, so feedback is very much
appreciated :)

Regards,

Mark
-------------
Mark Dunning
PhD Student
Computational Biology Group
Hutchison / MRC Research Centre
Department of Oncology
University of Cambridge
Hills Rd, Cambridge CB2 2XZ

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Giovanni
Coppola
Sent: 04 March 2006 16:54
To: Lynn Amon
Cc: Bioconductor
Subject: Re: [BioC] info su illumina


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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

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