Question about using lumi package
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Hu, Xin ▴ 10
@hu-xin-5213
Last seen 8.1 years ago
Hi, Dr. Pan, I am very impressive on lumi package that you developed and I am going to apply it to my HM450K dataset and put your paper as citation. Can I have a simple question on reading file? As your example file is different from what I got with HM450K file processed by GenomeStudio. Would you please tell me how to read HM450K file into Lumi and annotation library, what format of input file should I prepare? Idat file or csv file, which column is required to compatible with your package? How to prepare my HM450K data to the same format of example.lumiMethy? I appreciate so much for your great help! PhD student in MD Anderson Cancer Center Kathy (Xin Hu) [[alternative HTML version deleted]]
Cancer lumi Cancer lumi • 638 views
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Pan Du ▴ 440
@pan-du-4636
Last seen 8.1 years ago
Hi Xin The lumi package basically calls "methylumiR" function in methylumi package to import Infinium methylation file. The format of Infinium 450k data is the same as 27k data. I remember there is an example file in methylumi package. ?Please check it. If you have Illumina GenomeStudio or Beadstudio software, you should get the output easily. But please remember to output the intensity of ProbeA (methylated) and ProbeB (unmethylated), which are required for data normalization. Pan On Wed, Apr 11, 2012 at 3:00 AM, ?<bioconductor-request at="" r-project.org=""> wrote: > Message: 24 > Date: Tue, 10 Apr 2012 18:27:43 -0500 > From: "Hu, Xin" <xin.hu at="" uth.tmc.edu=""> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Question about using lumi package > Message-ID: > ? ? ? ?<f2df7bef9fb81f4997b7ae7191a14f660ff626cbb2 at="" uthcms3.uthouston.edu=""> > Content-Type: text/plain > > Hi, Dr. Pan, > I am very impressive on lumi package that you developed and I am going to apply it to my HM450K dataset and put your paper as citation. > > Can I have a simple question on reading file? As your example file is different from what I got with HM450K file processed by GenomeStudio. > Would you please tell me how to read HM450K file into Lumi and annotation library, what format of input file should I prepare? Idat file or csv file, which column is required to compatible with your package? > > How to prepare my HM450K data to the same format of example.lumiMethy? > > I appreciate so much for your great help! > > PhD student in MD Anderson Cancer Center > Kathy (Xin Hu) > > >
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