lumi **

Lumi is an ongoing project for Illumina microarray data analysis, including the design of a software package in R/Bioconductor and the discussion of microarray experiment design.

** an open source project at the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University.


Positive Control for Methylation Studies

Recently, methylation arrays have been introduced as an easy tool to scan the genome for methylation differences.

Without a positive control, how do you know your protocol is working?

Bock C, et al (PMID 16520826 ) reported one gene PDE9, to be highly methylated in lymphocytic DNA. It might be used as a positive control gene. Like so called house-keeping genes, the methylation of this gene, however, might be regulated under some special circumstances.

A second method calls for spike-in. One can artificially spiking his samples with SssI methylase methylated DNA. SssI methylates all CpG resides with high efficiency.

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