[BioC] LimmaGUI for illumina data

Mark Dunning md392 at cam.ac.uk
Sat Jun 3 09:37:47 CEST 2006

Hi Roy,

In our group we have been developed the beadarray R package for the analysis
of Illumina BeadArrays. It is able to read both the output from Illumina's
BeadStudio or the raw data if you have access to it. The objects it creates
are very similar in style to limma and affy and it is also very easy to
convert to ExpressionSet object types.

The package is available as part of the 1.8 release of Bioconductor
(http://bioconductor.org/packages/1.8/bioc/html/beadarray.html). There is
also a version in the developers section which we are adding to all the time
(recently we made significant improvements in the time taken to process bead
level data).

Please let me know if you have any further questions.



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Roy Williams
Sent: 25 May 2006 06:29
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] LimmaGUI for illumina data


I have 2 questions:
1. I would be really grateful to have a list of papers that cite limma -
does such a list exist? If so could someone send it to me.
2. I would like to use the limmaGUI or AffyLMGUI package with illumina
array data (www.illumina.com). Is this possible? Could I load a .RData
(or .lmn) data object which has just the column headers (experiments)
and gene names along with the data? I have been using limma from the
command line and it would help considerably to have a GUI which prints
HTML reports.

Many thanks for any advice you might be able to offer,


Roy Williams PhD
The Burnham Institute for Medical Research
Bioinformatics Shared Resource
Building 10 Offices 2405/6
3010 Science Park Road
San Diego, California
92121 USA

Tel: 858 646 3100 ext 3915
email: royw at burnham.org
web site: idmweb.burnham.org

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