[BioC] Illumina Methylation data

Pan Du dupan at northwestern.edu
Thu Sep 30 17:01:05 CEST 2010

Hi Grace

The developing version of lumi package has implemented functions of
background adjustment and color balance adjustment functions for Illumina
Infinium methylation microarrays. Please check the vignette,
methylationAnalysis.pdf for more details.
Here is the link:



On 9/30/10 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 27
> Date: Thu, 30 Sep 2010 11:40:20 +0800
> From: zhiqun tang <sisitzq at gmail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Illumina Methylation data
> Message-ID:
> <AANLkTik_fzR5+FtaaC5z_qZ4e4Z-_XBte7eiY1Z_r8Nr at mail.gmail.com>
> Content-Type: text/plain
> Dear AlI,
> I am very appreciate for your kidly help.
> I am working on the Illumina methylation27 data, I would like to combine two
> data from two plates. According to the Illumina's recommendation, "Background
> intensity computed from a set of negative controls was subtracted from each
> analytical data point. The ratio of fluorescent signals was then computed
> from the two alleles â = (max(M, 0))/(|U| + |M| + 100)."
> But a portion of my samples don't have the
> negative_control_Grn_Arg_intensity, some of them even don't have the
> negative_control_red_Arg_intensity.  In that case, how can I estimate the
> background intensity?
> I also know that there is a dye shifting which might effect the combination
> of two dataset. How do I evaluate this dye problem on one plate? How to
> correct them? Which software or tools should I consider? Thank you.
> Grace
> [[alternative HTML version deleted]]

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