[BioC] Bioconductor Digest, Vol 110, Issue 11

[Pan Du]

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)
>
>
>