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.


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!

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Digging deeper into PubMed

You searched PubMed using a keyword of "GATA". Bingo! 5,881 papers on this topic. What are you going to do with it? Read them one-by-one? You know it is going to ruin your postdoc life.

So, you need some bioinformatics tools for it!

Here is an analysis on the major topics of these 5,881 papers. It is clear that GATA is a transcription factor regulating cell differentiation.

An author analysis suggests the leading researchers in this field:

One step further, you ask yourself: if I get a paper on this topic, where sould I publish it? Here are some thoughts:Is "GATA" a hot topic over years? Absolutely!So, you asked, what is this wonderful tool? --- Anne O'Tate.

Another similar tool, e-LiSe, can be found at

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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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