data analysis of illumina infinium 450k bead chip methylation pipeline

[Shrinka Sen]

Hello
This is Shrinka from NIBMG, Kalyani, India. Recently I am doing data analysis of illumina infinium 450k bead chip for methylation. Is there any complete pipeline to analyse these data, which can take care all the essential factors regarding methylation.

[mastal]

data analysis of illumina infinium 450k bead chip methylation pipeline

Hi,

Have you tried the Bioconductor mailing list?

The latest archives are at,

https://stat.ethz.ch/pipermail/bioconductor/2013-April/date.html

Best wishes,
Maria

[Elsie]

Maria is right, for example see

http://www.bioconductor.org/

and

http://www.bioconductor.org/packages/release/bioc/html/minfi.html

[Shrinka Sen]

Hello
This is Shrinka from NIBMG, Kalyani, India. Recently I am doing data analysis of illumina infinium 450k bead chip for methylation.Thanks for your suggestions friends. I am trying different pipelines. Can you help me in another aspect. Beside raw data from Genome studio, illumina provides a list of control probes. Can you give me any idea in which step this data should be used and how?

[Elsie]

The control probes are used for quality control, to assess your arrays for any technical issues. Depending on what software you use, depends on how this information will be used. For example, if you look at the minfi package,you will see that you only need to use the raw data and minfi will extract the information about the control probes for you.