Data format for the Lumi Package

How to generate a microarray output file to be analyzed by the lumi package in bioconductor? From the Illumina BeadStudio software, select "> File> Export to GeneSpring > Group Probe Profile". A file called "Group Probe Profile.txt" will be generated. That's it!

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.