Loading Data into MethyAnalysis
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Guest User ★ 12k
@guest-user-4897
Last seen 8.1 years ago
I have successfully installed MethyAnalysis and I am not understanding how to load my data. The exampleMethyGenoSet RDA file doesn't give me too much information as to how I need to setup my own data. I am also unsure if this package is meant for the Illumina 450K microarray or the 27K. -- output of sessionInfo(): -- Sent via the guest posting facility at bioconductor.org.
Microarray methyAnalysis Microarray methyAnalysis • 1.3k views
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Pan Du ▴ 440
@pan-du-4636
Last seen 8.1 years ago
Hi Ranya The vignette of MethyAnalysis package needs to be further improved. I will update it within next couple of weeks when I have time. As for creating MethyGenoSet objects, you can either use MethyGenoSet() function or converted them from MethyLumiM objects using MethyLumiM2GenoSet function, which is what I use. Basically the work flow is preprocessing the methylation data in the lumi package and then converted it as MethyGenoSet class and do further analysis. Since the MethyAnalysis package is designed for chromosome location based analysis, 450k data or sequencing data is recommended. 27K data can still use some functions (like plotting the data) in the package, but other functions (like slidewindow differential methylation detection) is not useful for 27k data. Hope this is helpful to you. Pan On Wed, Jan 16, 2013 at 8:34 AM, Ranya [guest] <guest at="" bioconductor.org=""> wrote: > > I have successfully installed MethyAnalysis and I am not understanding how to load my data. The exampleMethyGenoSet RDA file doesn't give me too much information as to how I need to setup my own data. I am also unsure if this package is meant for the Illumina 450K microarray or the 27K. > > -- output of sessionInfo(): > > > > -- > Sent via the guest posting facility at bioconductor.org.
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Hello,

I want to perform DNA methylation analysis using the package. Although I successfully installed it, I can't even reach the sample data. This is frustrating and I feel dumb.

I have fed the following commands to the console:

 >source("https://bioconductor.org/biocLite.R")

>biocLite("cummeRbund")

Update all/some/none? [a/s/n]: 
>a

>biocLite("methyAnalysis")

Update all/some/none? [a/s/n]: 
>a

Here is where it fails;

>data(exampleMethyGenoSet)
Warning message:
In data(exampleMethyGenoSet) : data set ‘exampleMethyGenoSet’ not found.

I set my working directory as the folder where all methyAnalysis packages are. What am I doing wrong?

Efraim

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