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]]
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)
>
>
>
