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On 2/7/06 9:02 AM, "Alberto Goldoni" <alberto.goldoni at="" eurogene.org=""> wrote: > Hi guys, > > i have a little question for you: > > is it possible to analyze illumine arrays with R..? > > is there a specific package? As far as I know there is not a specific package for dealing with illumina arrays. However, they are single-channel arrays, so you can think of them as similar to Affy (in a superficial way). Reading the data in is pretty simple using read.table. Sean

On 2/7/06 10:45 AM, "Natalie P. Thorne" <npt22 at="" cam.ac.uk=""> wrote: > > See beadarray a developer package of Bioconductor specifically developed > for analysing both SAM and beadchip data from Illumina. The package has > capabilities for reading Tiff files and (using bead center information) > extracting bead level data rather than the bead summary data provided by > Illumina. > > You're welcome to forward this to the list, for some reason my responses > to the list get delayed by a few days (I think because I use a different > email address to send from). > > Natalie Thanks, Natalie. I had missed that one. I will forward to the list. Sean >>> is it possible to analyze illumine arrays with R..? >>> >>> is there a specific package? >> >> As far as I know there is not a specific package for dealing with illumina >> arrays. However, they are single-channel arrays, so you can think of them >> as similar to Affy (in a superficial way). Reading the data in is pretty >> simple using read.table. > > ______________________________ > Natalie Thorne, PhD > Research Associate > Computational Biology Group > Hutchison/MRC Research Centre > Department of Oncology > University of Cambridge > Hills Rd, Cambridge CB2 2XZ > > Email: npt22 at cam.ac.uk > Phone: +44 (0)1223 763381 > Fax : +44 (0)1223 763262 > ______________________________

Yes - see beadarray a develpment package of Bioconductor. Natalie On Tue, 7 Feb 2006, Alberto Goldoni wrote: > Hi guys, > > i have a little question for you: > > is it possible to analyze illumine arrays with R..? > > is there a specific package? > > Best wishes to everybody > > > > Dr Alberto Goldoni > Medical Genetics Unit > S. Orsola-Malpighi Hospital > Via Massarenti n.9, Pad 11 > 40100 Bologna, Italy > Mobile Phone: 338-4145970 > Fax: 051-636-4004 > <mailto:alberto.goldoni at="" eurogene.org=""> alberto.goldoni at eurogene.org > <http: www.eurogene.org=""> www.eurogene.org > <http: www.lagem.it=""> www.lagem.it > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- ______________________________ Natalie Thorne, PhD Research Associate Computational Biology Group Hutchison/MRC Research Centre Department of Oncology University of Cambridge Hills Rd, Cambridge CB2 2XZ Email: npt22 at cam.ac.uk Phone: +44 (0)1223 763381 Fax : +44 (0)1223 763262

Check this: http://www.bioconductor.org/packages/bioc/1.8/html/beadarray.html Kind regards Martino On 7 Feb 2006, at 14:02, Alberto Goldoni wrote: > Hi guys, > > i have a little question for you: > > is it possible to analyze illumine arrays with R..? > > is there a specific package? > > Best wishes to everybody > > > > Dr Alberto Goldoni > Medical Genetics Unit > S. Orsola-Malpighi Hospital > Via Massarenti n.9, Pad 11 > 40100 Bologna, Italy > Mobile Phone: 338-4145970 > Fax: 051-636-4004 > <mailto:alberto.goldoni at="" eurogene.org=""> alberto.goldoni at eurogene.org > <http: www.eurogene.org=""> www.eurogene.org > <http: www.lagem.it=""> www.lagem.it > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > --------------------------------------- Martino Barenco CoMPLEX 4, Stephenson Way London NW1 2HE Tel.: +44 20 7679 5088 Fax.: +44 20 7679 5052 (please specify "CoMPLEX") Email: m.barenco at ucl.ac.uk

I have some scripts to deal with Illumina GoldenGate SNP assay data and have plans to turn them into a package in the coming month(s) I have no experience yet with the Infinium arrays or the expression arrays. Jan Oosting -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Alberto Goldoni Sent: dinsdag 7 februari 2006 15:02 To: bioconductor at stat.math.ethz.ch Subject: [BioC] info su illumina Hi guys, i have a little question for you: is it possible to analyze illumine arrays with R..? is there a specific package? Best wishes to everybody Dr Alberto Goldoni Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 <mailto:alberto.goldoni at="" eurogene.org=""> alberto.goldoni at eurogene.org <http: www.eurogene.org=""> www.eurogene.org <http: www.lagem.it=""> www.lagem.it [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

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

------------------------------ Message: 5 Date: Tue, 7 Feb 2006 15:02:10 +0100 From: "Alberto Goldoni" <alberto.goldoni@eurogene.org> Subject: [BioC] info su illumina To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: <003101c62bef$168d1280$e0fda8c0 at ASUS> Content-Type: text/plain Hi guys, i have a little question for you: is it possible to analyze illumine arrays with R..? is there a specific package? Best wishes to everybody >Yes. It's called beadarray. http://www.bioconductor.org/packages/bioc/1.8/html/beadarray.html